Host Cells Containing Multiple Integrating Vectors

ABSTRACT

The present invention relates to the production of proteins in host cells, and more particularly to host cells containing multiple integrated copies of an integrating vector. Suitable integrating vectors for use in the present invention include retrovirus vectors, lentivirus vectors, transposon vectors, and adeno-associated virus vectors. Methods are provided in which the host cells are prepared by using the integrating vectors at a high multiplicity of infection. The host cells are useful for producing pharmaceutical proteins, variants of proteins for use in screening assays, and for direct use in high throughput screening.

This application claims priority to provisional appl. 60/215,925, filed3 Jul. 2000.

FIELD OF THE INVENTION

The present invention relates to the production of proteins in hostcells, and more particularly to host cells containing multipleintegrated copies of an integrating vector.

BACKGROUND OF THE INVENTION

The pharmaceutical biotechnology industry is based on the production ofrecombinant proteins in mammalian cells. These proteins are essential tothe therapeutic treatment of many diseases and conditions. In manycases, the market for these proteins exceeds a billion dollars a year.Examples of proteins produced recombinantly in mammalian cells includeerythropoietin, factor VIII, factor IX, and insulin. For many of theseproteins, expression in mammalian cells is preferred over expression inprokaryotic cells because of the need for correct post-translationalmodification (e.g., glycosylation or silation; see, e.g., U.S. Pat. No.5,721,121, incorporated herein by reference).

Several methods are known for creating host cells that expressrecombinant proteins. In the most basic methods, a nucleic acidconstruct containing a gene encoding a heterologous protein andappropriate regulatory regions is introduced into the host cell andallowed to integrate. Methods of introduction include calcium phosphateprecipitation, microinjection, lipofection, and electroporation. Inother methods, a selection scheme is used to amplify the introducednucleic acid construct. In these methods, the cells are co-transfectedwith a gene encoding an amplifiable selection marker and a gene encodinga heterologous protein (See, e.g., Schroder and Friedl, Biotech. Bioeng.53(6):547-59 [1997]). After selection of the initial tranformants, thetransfected genes are amplified by the stepwise increase of theselective agent (e.g., dihydrofolate reductase) in the culture medium.In some cases, the exogenous gene may be amplified several hundred-foldby these procedures. Other methods of recombinant protein expression inmammalian cells utilize transfection with episomal vectors (e.g.,plasmids).

Current methods for creating mammalian cell line for expression ofrecombinant proteins suffer from several drawbacks. (See, e.g., Mielkeet al., Biochem. 35:2239-52 [1996]). Episomal systems allow for highexpression levels of the recombinant protein, but are frequently onlystable for a short time period (See, e.g., Klehr and Bode, Mol. Genet.(Life Sci. Adv.) 7:47-52 [1988]). Mammalian cell lines containingintegrated exogenous genes are somewhat more stable, but there isincreasing evidence that stability depends on the presence of only a fewcopies or even a single copy of the exogenous gene.

Standard transfection techniques favor the introduction of multiplecopies of the transgene into the genome of the host cell. Multipleintegration of the transgene has, in many cases, proven to beintrinsically unstable. This intrinsic instability may be due to thecharacteristic head-to-tail mode of integration which promotes the lossof coding sequences by homologous recombination (See, e.g., Weidle etal., Gene 66:193-203 [1988]) especially when the transgenes aretranscribed (See, e.g., McBurney et al., Somatic Cell Molec. Genet.20:529-40 [1994]). Host cells also have epigenetic defense mechanismsdirected against multiple copy integration events. In plants, thismechanism has been termed “cosuppression.” (See, e.g., Allen et al.,Plant Cell 5:603-13 [1993]). Indeed, it is not uncommon that the levelof expression is inversely related to copy number. These observationsare consistent with findings that multiple copies of exogenous genesbecome inactivated by methylation (See, e.g., Mehtali et al., Gene91:179-84 [1990]) and subsequent mutagenesis (See, e.g., Kricker et al.,Proc. Natl. Acad. Sci. 89:1075-79 [1992]) or silenced by heterochromatinformation (See, e.g., Dorer and Henikoff, Cell 77:993-1002 [1994]).

Accordingly, what is needed in the art are improved methods for makinghost cells that express recombinant proteins. Preferably, the host cellswill be stable over extended periods of time and express the proteinencoded by a transgene at high levels.

SUMMARY OF THE INVENTION

The present invention relates to the production of proteins in hostcells, and more particularly to host cells containing multipleintegrated copies of an integrating vector. The present invention is notlimited to host cells transfected with a particular number ofintegrating vectors. Indeed, host cells containing a wide range ofintegrating vectors are contemplated. In some embodiments, the presentinvention provides a host cell comprising a genome containing preferablyat least about two integrated integrating vectors. In still furtherembodiments, the genome preferably comprises at least 3 integratedintegrating vectors and most preferably at least 4 integratedintegrating vectors, 5 integrated integrating vectors, 6 integratedintegrating vectors, 7 integrated integrating vectors, 10 integratedintegrating vectors, 15 integrated integrating vectors, 20 integratedintegrating vectors, or 50 integrated integrating vectors.

The present invention is not limited to host cells containing vectorsencoding a single protein of interest (i.e., exogenous protein). Indeed,it is contemplated that the host cells are transfected with vectorsencoding multiple proteins of interest. In some embodiments, theintegrating vector comprises at least two exogenous genes. In somepreferred embodiments, the at least two exogenous genes are arranged ina polycistronic sequence. In some particularly preferred embodiments,the at least two exogenous genes are separated by an internal ribosomeentry site. In other preferred embodiments, the at least two exogenousgenes are arranged in a polycistronic sequence. In still furtherembodiments, the two exogenous genes comprise a heavy chain of animmunoglobulin molecule and a light chain of an immunoglobulin molecule.In other embodiments, one of the at least two exogenous genes is aselectable marker. In still other embodiments, the host cells compriseat least 2 integrated copies of a first integrating vector comprising afirst exogenous gene, and at least 1 integrated copy of a secondintegrating vector or other vector comprising a second exogenous gene.In still further embodiments, the host cells comprise at least 10integrated copies of a first integrating vector comprising a firstexogenous gene, and at least 1 integrated copy of a second integratingvector or other vector comprising a second exogenous gene.

In some preferred embodiments, the integrating vectors comprise at leastone exogenous gene operably linked to a promoter. The present inventionis not limited to vectors containing a particular promoter. Indeed, avariety of promoters are contemplated. In some embodiments of thepresent invention, the promoter is selected from the group consisting ofthe alpha-lactalbumin promoter, cytomegalovirus promoter and the longterminal repeat of Moloney murine leukemia virus. In other preferredembodiments, the integrating vectors further comprise a secretion signaloperably linked to the exogenous gene. In still other embodiments, theintegrating vectors further comprise an RNA export element operablylinked to the exogenous gene.

The present invention is not limited to a particular integrating vector.Indeed, a variety of integrating vectors are contemplated. In someembodiments of the present invention, the integrating vector is selectedfrom the group consisting of a retroviral vector, a lentiviral vector,and a transposon vector. In some preferred embodiments, the retroviralvector is a pseudotyped retroviral vector. In other preferredembodiments, the pseudotyped retroviral vector comprises a Gglycoprotein. The retroviral vectors of the present invention are notlimited to a particular G glycoprotein. Indeed, a variety of Gglycoproteins are contemplated. In some particularly preferredembodiments, the G glycoprotein is selected from the group consisting ofvesicular stomatitis virus, Piry virus, Chandipura virus, Spring viremiaof carp virus and Mokola virus G glycoproteins. In still furtherembodiments, the retroviral vector comprises long terminal repeats. Theretroviral vectors of the present invention are not limited to aparticular LTR. Indeed, a variety of LTRs are contemplated, including,but not limited to MoMLV, MoMuSV, MMTV long terminal repeats.

In other embodiments, the retroviral vector is a lentiviral vector. Insome preferred embodiments, the lentiviral vector is pseudotyped. Insome particularly preferred embodiments, the lentiviral vector comprisesa G glycoprotein. In still further embodiments, the G glycoprotein isselected from the group consisting of vesicular stomatitis virus, Piryvirus, Chandipura virus, Spring viremia of carp virus and Mokola virus Gglycoproteins. In still other embodiments, the lentiviral vectorcomprises long terminal repeats selected from the group consisting ofHIV and equine infectious anemia long terminal repeats.

In still further embodiments of the present invention, the integratingvector is a transposon vector. In some preferred embodiments, thetransposon vector is selected from Tn5, Tn7, and Tn10 transposonvectors.

The present invention is not limited to a particular host cell. Indeed,a variety of host cells are contemplated. In some embodiments of thepresent invention, the host cell is cultured in vitro. In still furtherembodiments of the present invention, the host cell is selected fromchinese hamster ovary cells, baby hamster kidney cells, and bovinemammary epithelial cells. In some preferred embodiments, the host cellsare clonally derived. In other embodiments, the host cells arenon-clonally derived. In some embodiments, the genome of the host cellis stable for greater than 10 passages. In other embodiments, the genomeis stable for greater than 50 passages, while in still otherembodiments, the genome is stable for greater than 100 passages. Instill other embodiments, the host cells can be an embryonic stem cell,oocyte, or embryo. In some embodiments, the integrated vector is stablein the absence of selection.

The present invention is not limited to vectors encoding a particularprotein of interest. Indeed, vectors encoding a variety of proteins ofinterest encoded by exogenous genes are contemplated. In someembodiments, the protein of interest is selected from hepatitis Bsurface antigen, MN14 antibody, LL2 antibody, botulinum toxin antibodyand cc49IL2. In some embodiments, the genes encoding the protein ofinterest are intronless, while in other embodiments, the genes encodingthe protein of interest include at least one intron.

The present invention also provides a method for transfecting ortransducing host cells comprising: 1) providing: a) a host cellcomprising a genome, and b) a plurality of integrating vectors; and 2)contacting the host cell with the plurality of integrating vectors underconditions such that at least two integrating vectors integrate into thegenome of the host cell. In some embodiments, the conditions comprisecontacting the host cells at a multiplicity of infection of greater than10. In other embodiments, the conditions comprise contacting the hostcells at a multiplicity of infection of from about 10 to 1,000,000. Instill further embodiments, the conditions comprise contacting the hostcells at a multiplicity of infection of from about 100 to 10,000. Instill further embodiments, the conditions comprise contacting the hostcells at a multiplicity of infection of from about 100 to 1,000. Instill other embodiments of the present invention, the method furthercomprises transfecting said host cells with at least two integratingvectors, each of said two integrating comprising a different exogenousgene. In still other embodiments, the conditions comprise serialtransfection or transduction or host cells wherein the host cells aretransfected or transduced in at least a first transfection ortransduction with a vector encoding a protein of interest and thenre-transfected or re-transduced in a separate transfection ortransduction step.

The present invention further provides a method of producing a proteinof interest comprising: 1) providing a host cell comprising a genome,the genome comprising at least two integrated copies of at least oneintegrating vector comprising an exogenous gene operably linked to apromotor, wherein the exogenous gene encodes a protein of interest, and2) culturing the host cells under conditions such that the protein ofinterest is produced. In some preferred embodiments, the integratingvector further comprises a secretion signal sequence operably linked tosaid exogenous gene. In other embodiments, the methods further comprisestep 3) isolating the protein of interest. The present invention is notlimited to any particular culture system. Indeed, a variety of culturesystems are contemplated, including, but not limited to roller bottlecultures, perfusion cultures, batch fed cultures, and petri dishcultures. In some embodiments, the cell line is clonally selected, whilein other embodiments, the cells are non-clonally selected.

The methods of the present invention are not limited to host cellscontaining any particular number of integrated integrating vectors.Indeed, in some embodiments, the genome of the host cell comprisesgreater than 3 integrated copies of the integrating vector; in otherembodiments, genome of the host cell comprises greater than 4 integratedcopies of the integrating vector.; in still other embodiments, thegenome of the host cell comprises greater than 5 integrated copies ofthe integrating vector; in further embodiments, the genome of the hostcell comprises greater than 7 integrated copies of the integratingvector; while in still further embodiments, the genome of the host cellcomprises greater than 10 integrated copies of the integrating vector.In other embodiments, the genome of the host cell comprises betweenabout 2 and 20 integrated copies of the integrating vector. In someembodiments, the genome of the host cell comprises between about 3 and10 integrated copies of the integrating vector.

The methods of the present invention are not limited to any particularintegrating vector. Indeed, the use of a variety of integrating vectorsis contemplated. In some embodiments, the integrating vector is aretroviral vector. In some preferred embodiments, the retroviral vectoris a pseudotyped retroviral vector. In other embodiments, the retroviralvector is a lentiviral vector.

The methods of the present invention are not limited to the use of anyparticular host cell. Indeed, the use of a variety of host cells iscontemplated, including, but not limited to, Chinese hamster ovarycells, baby hamster kidney cells, bovine mammary epithelial cells,oocytes, embryos, stem cells, and embryonic stem cells.

The methods of the present invention are not limited to the productionof any particular amount of exogenous protein (i.e., protein ofinterest) from the host cells. Indeed, it is contemplated that a varietyof expression levels are acceptable from the methods of the presentinvention. In some embodiments, the host cells synthesize greater thanabout 1 picogram per cell per day of the protein of interest. In otherembodiments, the host cells synthesize greater than about 10 picogramsper cell per day of the protein of interest. In still furtherembodiments, the host cells synthesize greater than about 50 picogramsper cell per day of the protein of interest.

In other embodiments, the present invention provides a method forscreening compounds comprising: 1) providing a) a host cell comprising agenome, the genome comprising at least two integrated copies of at leastone integrating vector comprising an exogenous gene operably linked to apromotor, wherein the exogenous gene encodes a protein of interest; andb) one or more test compounds; 2) culturing the host cells underconditions such that the protein of interest is expressed; 3) treatingthe host cells with one or more test compounds; and 4) assaying for thepresence or absence of a response in the host cells to the testcompound. In some embodiments of the present invention, the exogenousgene encodes a protein selected from the group consisting of reporterproteins, membrane receptor proteins, nucleic acid binding proteins,cytoplasmic receptor proteins, ion channel proteins, signal transductionproteins, protein kinases, protein phosphatases, and proteins encoded byoncogenes.

In still further embodiments, the host cell further comprises a reportergene. In some particularly preferred embodiments, the reporter gene isselected from the group consisting of green fluorescent protein,luciferase, beta-galactosidase, and beta-lactamase. In some embodiments,the assaying step further comprises detecting a signal from the reportergene. In other embodiments, the genome of the host cell comprises atleast two integrating vectors, each comprising a different exogenousgene.

In still other embodiments, the present invention provides methods forcomparing protein activity comprising: 1) providing a) a first host cellcomprising a first integrating vector comprising a promoter operably toa first exogenous gene, wherein the first exogenous gene encodes a firstprotein of interest, and b) at least a second host cell comprising asecond integrating vector comprising a promoter operably linked to asecond exogenous gene, wherein the second exogenous gene encodes asecond exogenous gene that is a variant of the first protein ofinterest; 2) culturing the host cells under conditions such that thefirst and second proteins of interest are produced; and 3) comparing theactivities of the first and second proteins of interest.

In some embodiments, the exogenous gene encodes a protein selected fromthe group consisting of membrane receptor proteins, nucleic acid bindingproteins, cytoplasmic receptor proteins, ion channel proteins, signaltransduction proteins, protein kinases, protein phosphatases, cell cycleproteins, and proteins encoded by oncogenes. In other embodiments, thefirst and second proteins of interest differ by a single amino acid. Instill further embodiments, the first and second proteins of interest aregreater than 95% identical, preferably greater than 90% identical, andmost preferably greater than 80% identical.

In other embodiments, the present invention provides methodscomprising: 1) providing: a) a host cell comprising a genome comprisingat least one integrated exogenous gene; and b) a plurality ofintegrating vectors; and 2) contacting the host cell with the pluralityof integrating vectors under conditions such that at least two of theintegrating vectors integrate into the genome of the host cell. In someembodiments, the integrated exogenous gene comprises an integratingvector. In other embodiments, the host cell is clonally selected. Inalternative embodiments, the host cell is non-clonally selected.

In still further embodiments, the present invention provides methods ofindirectly detecting the expression of a protein of interest comprisingproviding a host cell transfected with a vector encoding a polycistronicsequence, wherein the polycistronic sequence comprises a signal proteinand a protein of interest operably linked by an IRES, and culturing thehost cells under conditions such that the signal protein and protein ofinterest are produced, wherein the presence of the signal proteinindicates the presence of the protein of interest. The methods of thepresent invention are not limited to the expression of any particularprotein of interest. Indeed, the expression of a variety of proteins ofinterest is contemplated, including, but not limited to, G-proteincoupled receptors. The present invention is not limited to the use ofany particular signal protein. Indeed, the use of variety of signalproteins is contemplated, including, but not limited to, immunoglobulinheavy and light chains, beta-galactosidase, beta-lactamase, greenfluorescent protein, and luciferase. In particularly preferredembodiments, expression of the signal protein and protein of interest isdriven by the same promoter and the signal protein and protein ofinterest are transcribed as a single transcriptional unit.

DESCRIPTION OF THE FIGURES

FIG. 1 is a western blot of a 15% SDS-PAGE gel run under denaturingconditions and probed with anti-human IgG (Fc) and anti-human IgG(Kappa).

FIG. 2 is a graph of MN14 expression over time.

FIG. 3 is a Western blot of a 15% PAGE run under non-denaturingconditions and probed with anti-human IgG (Fc) and anti-human IgG(Kappa).

FIG. 4 provides the sequence for the hybrid human-bovinealpha-lactalbumin promoter (SEQ ID NO:1).

FIG. 5 provides the sequence for the mutated PPE sequence (SEQ ID NO:2).

FIG. 6 provides the sequence for the IRES-Signal peptide sequence (SEQID NO:3).

FIGS. 7 a and 7 b provide the sequence for CMV MN14 vector (SEQ IDNO:4).

FIGS. 8 a and 8 b provide the sequence for the CMV LL2 vector (SEQ IDNO:5).

FIGS. 9 a-c provide the sequence for the MMTV MN14 vector (SEQ ID NO:6).

FIGS. 10 a-d provide the sequence for the alpha-lactalbumin MN14 Vector(SEQ ID NO:7).

FIGS. 11 a-c provide the sequence for the alpha-lactalbumin Bot vector(SEQ ID NO:8).

FIGS. 12 a-b provide the sequence for the LSRNL vector (SEQ ID NO:9).

FIGS. 13 a-b provide the sequence for the alpha-lactalbumin cc49IL2vector (SEQ ID NO:10).

FIGS. 14 a-c provides the sequence for the alpha-lactalbumin YP vector(SEQ ID NO:11).

FIG. 15 provides the sequence for the IRES-Casein signal peptidesequence (SEQ ID NO:12).

FIGS. 16 a-c provide the sequence for the LNBOTDC vector (SEQ ID NO:13).

FIG. 17 provides a graph depicting the INVADER Assay gene ratio in CMVpromoter cell lines.

FIG. 18 provides a graph depicting the INVADER Assay gene ratio inα-lactalbumin promotor cell lines.

FIGS. 19 a-d provide the sequence of a retroviral vector that expressesa G-Protein coupled receptor and antibody light chain.

DEFINITIONS

To facilitate understanding of the invention, a number of terms aredefined below.

As used herein, the term “host cell” refers to any eukaryotic cell(e.g., mammalian cells, avian cells, amphibian cells, plant cells, fishcells, and insect cells), whether located in vitro or in vivo.

As used herein, the term “cell culture” refers to any in vitro cultureof cells. Included within this term are continuous cell lines (e.g.,with an immortal phenotype), primary cell cultures, finite cell lines(e.g., non-transformed cells), and any other cell population maintainedin vitro, including oocytes and embryos.

As used herein, the term “vector” refers to any genetic element, such asa plasmid, phage, transposon, cosmid, chromosome, virus, virion, etc.,which is capable of replication when associated with the proper controlelements and which can transfer gene sequences between cells. Thus, theterm includes cloning and expression vehicles, as well as viral vectors.

As used herein, the term “integrating vector” refers to a vector whoseintegration or insertion into a nucleic acid (e.g., a chromosome) isaccomplished via an integrase. Examples of “integrating vectors”include, but are not limited to, retroviral vectors, transposons, andadeno associated virus vectors.

As used herein, the term “integrated” refers to a vector that is stablyinserted into the genome (i.e., into a chromosome) of a host cell.

As used herein, the term “multiplicity of infection” or “MOI” refers tothe ratio of integrating vectors:host cells used during transfection ortransduction of host cells. For example, if 1,000,000 vectors are usedto transduce 100,000 host cells, the multiplicity of infection is 10.The use of this term is not limited to events involving transduction,but instead encompasses introduction of a vector into a host by methodssuch as lipofection, microinjection, calcium phosphate precipitation,and electroporation.

As used herein, the term “genome” refers to the genetic material (e.g.,chomosomes) of an organism.

The term “nucleotide sequence of interest” refers to any nucleotidesequence (e.g., RNA or DNA), the manipulation of which may be deemeddesirable for any reason (e.g., treat disease, confer improvedqualities, expression of a protein of interest in a host cell,expression of a ribozyme, etc.), by one of ordinary skill in the art.Such nucleotide sequences include, but are not limited to, codingsequences of structural genes (e.g., reporter genes, selection markergenes, oncogenes, drug resistance genes, growth factors, etc.), andnon-coding regulatory sequences which do not encode an mRNA or proteinproduct (e.g., promoter sequence, polyadenylation sequence, terminationsequence, enhancer sequence, etc.).

As used herein, the term “protein of interest” refers to a proteinencoded by a nucleic acid of interest.

As used herein, the term “signal protein” refers to a protein that isco-expressed with a protein of interest and which, when detected by asuitable assay, provides indirect evidence of expression of the proteinof interest. Examples of signal protein useful in the present inventioninclude, but are not limited to, immunoglobulin heavy and light chains,beta-galactosidase, beta-lactamase, green fluorescent protein, andluciferase.

As used herein, the term “exogenous gene” refers to a gene that is notnaturally present in a host organism or cell, or is artificiallyintroduced into a host organism or cell.

The term “gene” refers to a nucleic acid (e.g., DNA or RNA) sequencethat comprises coding sequences necessary for the production of apolypeptide or precursor (e.g., proinsulin). The polypeptide can beencoded by a full length coding sequence or by any portion of the codingsequence so long as the desired activity or functional properties (e.g.,enzymatic activity, ligand binding, signal transduction, etc.) of thefull-length or fragment are retained. The term also encompasses thecoding region of a structural gene and includes sequences locatedadjacent to the coding region on both the 5′ and 3′ ends for a distanceof about 1 kb or more on either end such that the gene corresponds tothe length of the full-length mRNA. The sequences that are located 5′ ofthe coding region and which are present on the mRNA are referred to as5′ untranslated sequences. The sequences that are located 3′ ordownstream of the coding region and which are present on the mRNA arereferred to as 3′ untranslated sequences. The term “gene” encompassesboth cDNA and genomic forms of a gene. A genomic form or clone of a genecontains the coding region interrupted with non-coding sequences termed“introns” or “intervening regions” or “intervening sequences.” Intronsare segments of a gene which are transcribed into nuclear RNA (hnRNA);introns may contain regulatory elements such as enhancers. Introns areremoved or “spliced out” from the nuclear or primary transcript; intronstherefore are absent in the messenger RNA (mRNA) transcript. The mRNAfunctions during translation to specify the sequence or order of aminoacids in a nascent polypeptide.

As used herein, the term “gene expression” refers to the process ofconverting genetic information encoded in a gene into RNA (e.g., mRNA,rRNA, tRNA, or snRNA) through “transcription” of the gene (i.e., via theenzymatic action of an RNA polymerase), and for protein encoding genes,into protein through “translation” of mRNA. Gene expression can beregulated at many stages in the process. “Up-regulation” or “activation”refers to regulation that increases the production of gene expressionproducts (i.e., RNA or protein), while “down-regulation” or “repression”refers to regulation that decrease production. Molecules (e.g.,transcription factors) that are involved in up-regulation ordown-regulation are often called “activators” and “repressors,”respectively.

Where “amino acid sequence” is recited herein to refer to an amino acidsequence of a naturally occurring protein molecule, “amino acidsequence” and like terms, such as “polypeptide” or “protein” are notmeant to limit the amino acid sequence to the complete, native aminoacid sequence associated with the recited protein molecule.

As used herein, the terms “nucleic acid molecule encoding,” “DNAsequence encoding,” “DNA encoding,” “RNA sequence encoding,” and “RNAencoding” refer to the order or sequence of deoxyribonucleotides orribonucleotides along a strand of deoxyribonucleic acid or ribonucleicacid. The order of these deoxyribonucleotides or ribonucleotidesdetermines the order of amino acids along the polypeptide (protein)chain. The DNA or RNA sequence thus codes for the amino acid sequence.

As used herein, the term “variant,” when used in reference to a protein,refers to proteins encoded by partially homologous nucleic acids so thatthe amino acid sequence of the proteins varies. As used herein, the term“variant” encompasses proteins encoded by homologous genes having bothconservative and nonconservative amino acid substitutions that do notresult in a change in protein function, as well as proteins encoded byhomologous genes having amino acid substitutions that cause decreased(e.g., null mutations) protein function or increased protein function.

As used herein, the terms “complementary” or “complementarity” are usedin reference to polynucleotides (i.e., a sequence of nucleotides)related by the base-pairing rules. For example, for the sequence“A-G-T,” is complementary to the sequence “T-C-A.” Complementarity maybe “partial,” in which only some of the nucleic acids' bases are matchedaccording to the base pairing rules. Or, there may be “complete” or“total” complementarity between the nucleic acids. The degree ofcomplementarity between nucleic acid strands has significant effects onthe efficiency and strength of hybridization between nucleic acidstrands. This is of particular importance in amplification reactions, aswell as detection methods that depend upon binding between nucleicacids.

The terms “homology” and “percent identity” when used in relation tonucleic acids refers to a degree of complementarity. There may bepartial homology (i.e., partial identity) or complete homology (i.e.,complete identity). A partially complementary sequence is one that atleast partially inhibits a completely complementary sequence fromhybridizing to a target nucleic acid sequence and is referred to usingthe functional term “substantially homologous.” The inhibition ofhybridization of the completely complementary sequence to the targetsequence may be examined using a hybridization assay (Southern orNorthern blot, solution hybridization and the like) under conditions oflow stringency. A substantially homologous sequence or probe (i.e., anoligonucleotide which is capable of hybridizing to anotheroligonucleotide of interest) will compete for and inhibit the binding(i.e., the hybridization) of a completely homologous sequence to atarget sequence under conditions of low stringency. This is not to saythat conditions of low stringency are such that non-specific binding ispermitted; low stringency conditions require that the binding of twosequences to one another be a specific (i.e., selective) interaction.The absence of non-specific binding may be tested by the use of a secondtarget which lacks even a partial degree of complementarity (e.g., lessthan about 30% identity); in the absence of non-specific binding theprobe will not hybridize to the second non-complementary target.

The art knows well that numerous equivalent conditions may be employedto comprise low stringency conditions; factors such as the length andnature (DNA, RNA, base composition) of the probe and nature of thetarget (DNA, RNA, base composition, present in solution or immobilized,etc.) and the concentration of the salts and other components (e.g., thepresence or absence of formamide, dextran sulfate, polyethylene glycol)are considered and the hybridization solution may be varied to generateconditions of low stringency hybridization different from, butequivalent to, the above listed conditions. In addition, the art knowsconditions that promote hybridization under conditions of highstringency (e.g., increasing the temperature of the hybridization and/orwash steps, the use of formamide in the hybridization solution, etc.).

When used in reference to a double-stranded nucleic acid sequence suchas a cDNA or genomic clone, the term “substantially homologous” refersto any probe that can hybridize to either or both strands of thedouble-stranded nucleic acid sequence under conditions of low stringencyas described above.

When used in reference to a single-stranded nucleic acid sequence, theterm “substantially homologous” refers to any probe that can hybridize(i.e., it is the complement of) the single-stranded nucleic acidsequence under conditions of low stringency as described above.

As used herein, the term “hybridization” is used in reference to thepairing of complementary nucleic acids. Hybridization and the strengthof hybridization (i.e., the strength of the association between thenucleic acids) is impacted by such factors as the degree ofcomplementary between the nucleic acids, stringency of the conditionsinvolved, the T_(m) of the formed hybrid, and the G:C ratio within thenucleic acids. A single molecule that contains pairing of complementarynucleic acids within its structure is said to be “self-hybridized.”

As used herein, the term “T_(m)” is used in reference to the “meltingtemperature” of a nucleic acid. The melting temperature is thetemperature at which a population of double-stranded nucleic acidmolecules becomes half dissociated into single strands. The equation forcalculating the T_(m) of nucleic acids is well known in the art. Asindicated by standard references, a simple estimate of the T_(m) valuemay be calculated by the equation: T_(m)=81.5+0.41 (% G+C), when anucleic acid is in aqueous solution at 1 M NaCl (See e.g., Anderson andYoung, Quantitative Filter Hybridization, in Nucleic Acid Hybridization[1985]). Other references include more sophisticated computations thattake structural as well as sequence characteristics into account for thecalculation of T_(m).

As used herein the term “stringency” is used in reference to theconditions of temperature, ionic strength, and the presence of othercompounds such as organic solvents, under which nucleic acidhybridizations are conducted. With “high stringency” conditions, nucleicacid base pairing will occur only between nucleic acid fragments thathave a high frequency of complementary base sequences. Thus, conditionsof “weak” or “low” stringency are often required with nucleic acids thatare derived from organisms that are genetically diverse, as thefrequency of complementary sequences is usually less.

“High stringency conditions” when used in reference to nucleic acidhybridization comprise conditions equivalent to binding or hybridizationat 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/lNaH₂PO₄.H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS,5×Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followedby washing in a solution comprising 0.1×SSPE, 1.0% SDS at 42° C. when aprobe of about 500 nucleotides in length is employed.

“Medium stringency conditions” when used in reference to nucleic acidhybridization comprise conditions equivalent to binding or hybridizationat 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/lNaH₂PO₄.H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS,5×Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followedby washing in a solution comprising 1.0×SSPE, 1.0% SDS at 42° C. when aprobe of about 500 nucleotides in length is employed.

“Low stringency conditions” comprise conditions equivalent to binding orhybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/lNaCl, 6.9 g/l NaH₂PO₄.H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 withNaOH), 0.1% SDS, 5×Denhardt's reagent [50×Denhardt's contains per 500ml: 5 g Ficoll (Type 400, Pharamcia), 5 g BSA (Fraction V; Sigma)] and100 μg/ml denatured salmon sperm DNA followed by washing in a solutioncomprising 5×SSPE, 0.1% SDS at 42° C. when a probe of about 500nucleotides in length is employed.

A gene may produce multiple RNA species that are generated bydifferential splicing of the primary RNA transcript. cDNAs that aresplice variants of the same gene will contain regions of sequenceidentity or complete homology (representing the presence of the sameexon or portion of the same exon on both cDNAs) and regions of completenon-identity (for example, representing the presence of exon “A” on cDNA1 wherein cDNA 2 contains exon “B” instead). Because the two cDNAscontain regions of sequence identity they will both hybridize to a probederived from the entire gene or portions of the gene containingsequences found on both cDNAs; the two splice variants are thereforesubstantially homologous to such a probe and to each other.

The terms “in operable combination,” “in operable order,” and “operablylinked” as used herein refer to the linkage of nucleic acid sequences insuch a manner that a nucleic acid molecule capable of directing thetranscription of a given gene and/or the synthesis of a desired proteinmolecule is produced. The term also refers to the linkage of amino acidsequences in such a manner so that a functional protein is produced.

As used herein, the term “selectable marker” refers to a gene thatencodes an enzymatic activity that confers the ability to grow in mediumlacking what would otherwise be an essential nutrient (e.g. the HIS3gene in yeast cells); in addition, a selectable marker may conferresistance to an antibiotic or drug upon the cell in which theselectable marker is expressed. Selectable markers may be “dominant”; adominant selectable marker encodes an enzymatic activity that can bedetected in any eukaryotic cell line. Examples of dominant selectablemarkers include the bacterial aminoglycoside 3′ phosphotransferase gene(also referred to as the neo gene) that confers resistance to the drugG418 in mammalian cells, the bacterial hygromycin G phosphotransferase(hyg) gene that confers resistance to the antibiotic hygromycin and thebacterial xanthine-guanine phosphoribosyl transferase gene (alsoreferred to as the gpt gene) that confers the ability to grow in thepresence of mycophenolic acid. Other selectable markers are not dominantin that their use must be in conjunction with a cell line that lacks therelevant enzyme activity. Examples of non-dominant selectable markersinclude the thymidine kinase (tk) gene that is used in conjunction withtk⁻ cell lines, the CAD gene which is used in conjunction withCAD-deficient cells and the mammalian hypoxanthine-guaninephosphoribosyl transferase (hprt) gene which is used in conjunction withhprt⁻ cell lines. A review of the use of selectable markers in mammaliancell lines is provided in Sambrook, J. et al., Molecular Cloning: ALaboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, NewYork (1989) pp. 16.9-16.15.

As used herein, the term “regulatory element” refers to a geneticelement which controls some aspect of the expression of nucleic acidsequences. For example, a promoter is a regulatory element thatfacilitates the initiation of transcription of an operably linked codingregion. Other regulatory elements are splicing signals, polyadenylationsignals, termination signals, RNA export elements, internal ribosomeentry sites, etc. (defined infra).

Transcriptional control signals in eukaryotes comprise “promoter” and“enhancer” elements. Promoters and enhancers consist of short arrays ofDNA sequences that interact specifically with cellular proteins involvedin transcription (Maniatis et al., Science 236:1237 [1987]). Promoterand enhancer elements have been isolated from a variety of eukaryoticsources including genes in yeast, insect and mammalian cells, andviruses (analogous control elements, i.e., promoters, are also found inprokaryotes). The selection of a particular promoter and enhancerdepends on what cell type is to be used to express the protein ofinterest. Some eukaryotic promoters and enhancers have a broad hostrange while others are functional in a limited subset of cell types (forreview see, Voss et al., Trends Biochem. Sci., 11:287 [1986]; andManiatis et al., supra). For example, the SV40 early gene enhancer isvery active in a wide variety of cell types from many mammalian speciesand has been widely used for the expression of proteins in mammaliancells (Dijkema et al., EMBO J. 4:761 [1985]). Two other examples ofpromoter/enhancer elements active in a broad range of mammalian celltypes are those from the human elongation factor 1α gene (Uetsuki etal., J. Biol. Chem., 264:5791 [1989]; Kim et al., Gene 91:217 [1990];and Mizushima and Nagata, Nuc. Acids. Res., 18:5322 [1990]) and the longterminal repeats of the Rous sarcoma virus (Gorman et al., Proc. Natl.Acad. Sci. USA 79:6777 [1982]) and the human cytomegalovirus (Boshart etal., Cell 41:521 [1985]).

As used herein, the term “promoter/enhancer” denotes a segment of DNAwhich contains sequences capable of providing both promoter and enhancerfunctions (i.e., the functions provided by a promoter element and anenhancer element, see above for a discussion of these functions). Forexample, the long terminal repeats of retroviruses contain both promoterand enhancer functions. The enhancer/promoter may be “endogenous” or“exogenous” or “heterologous.” An “endogenous” enhancer/promoter is onewhich is naturally linked with a given gene in the genome. An“exogenous” or “heterologous” enhancer/promoter is one which is placedin juxtaposition to a gene by means of genetic manipulation (i.e.,molecular biological techniques such as cloning and recombination) suchthat transcription of that gene is directed by the linkedenhancer/promoter.

Regulatory elements may be tissue specific or cell specific. The term“tissue specific” as it applies to a regulatory element refers to aregulatory element that is capable of directing selective expression ofa nucleotide sequence of interest to a specific type of tissue (e.g.,liver) in the relative absence of expression of the same nucleotidesequence of interest in a different type of tissue (e.g., lung).

Tissue specificity of a regulatory element may be evaluated by, forexample, operably linking a reporter gene to a promoter sequence (whichis not tissue-specific) and to the regulatory element to generate areporter construct, introducing the reporter construct into the genomeof an animal such that the reporter construct is integrated into everytissue of the resulting transgenic animal, and detecting the expressionof the reporter gene (e.g., detecting mRNA, protein, or the activity ofa protein encoded by the reporter gene) in different tissues of thetransgenic animal. The detection of a greater level of expression of thereporter gene in one or more tissues relative to the level of expressionof the reporter gene in other tissues shows that the regulatory elementis “specific” for the tissues in which greater levels of expression aredetected. Thus, the term “tissue-specific” (e.g., liver-specific) asused herein is a relative term that does not require absolutespecificity of expression. In other words, the term “tissue-specific”does not require that one tissue have extremely high levels ofexpression and another tissue have no expression. It is sufficient thatexpression is greater in one tissue than another. By contrast, “strict”or “absolute” tissue-specific expression is meant to indicate expressionin a single tissue type (e.g., liver) with no detectable expression inother tissues.

The term “cell type specific” as applied to a regulatory element refersto a regulatory element which is capable of directing selectiveexpression of a nucleotide sequence of interest in a specific type ofcell in the relative absence of expression of the same nucleotidesequence of interest in a different type of cell within the same tissue.The term “cell type specific” when applied to a regulatory element alsomeans a regulatory element capable of promoting selective expression ofa nucleotide sequence of interest in a region within a single tissue.

Cell type specificity of a regulatory element may be assessed usingmethods well known in the art (e.g., immunohistochemical staining and/orNorthern blot analysis). Briefly, for immunohistochemical staining,tissue sections are embedded in paraffin, and paraffin sections arereacted with a primary antibody specific for the polypeptide productencoded by the nucleotide sequence of interest whose expression isregulated by the regulatory element. A labeled (e.g., peroxidaseconjugated) secondary antibody specific for the primary antibody isallowed to bind to the sectioned tissue and specific binding detected(e.g., with avidin/biotin) by microscopy. Briefly, for Northern blotanalysis, RNA is isolated from cells and electrophoresed on agarose gelsto fractionate the RNA according to size followed by transfer of the RNAfrom the gel to a solid support (e.g., nitrocellulose or a nylonmembrane). The immobilized RNA is then probed with a labeledoligo-deoxyribonucleotide probe or DNA probe to detect RNA speciescomplementary to the probe used. Northern blots are a standard tool ofmolecular biologists.

The term “promoter,” “promoter element,” or “promoter sequence” as usedherein, refers to a DNA sequence which when ligated to a nucleotidesequence of interest is capable of controlling the transcription of thenucleotide sequence of interest into mRNA. A promoter is typically,though not necessarily, located 5′ (i.e., upstream) of a nucleotidesequence of interest whose transcription into mRNA it controls, andprovides a site for specific binding by RNA polymerase and othertranscription factors for initiation of transcription.

Promoters may be constitutive or regulatable. The term “constitutive”when made in reference to a promoter means that the promoter is capableof directing transcription of an operably linked nucleic acid sequencein the absence of a stimulus (e.g., heat shock, chemicals, etc.). Incontrast, a “regulatable” promoter is one which is capable of directinga level of transcription of an operably linked nucleic acid sequence inthe presence of a stimulus (e.g., heat shock, chemicals, etc.) which isdifferent from the level of transcription of the operably linked nucleicacid sequence in the absence of the stimulus.

The presence of “splicing signals” on an expression vector often resultsin higher levels of expression of the recombinant transcript. Splicingsignals mediate the removal of introns from the primary RNA transcriptand consist of a splice donor and acceptor site (Sambrook et al.,Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring HarborLaboratory Press, New York [1989], pp. 16.7-16.8). A commonly usedsplice donor and acceptor site is the splice junction from the 16S RNAof SV40.

Efficient expression of recombinant DNA sequences in eukaryotic cellsrequires expression of signals directing the efficient termination andpolyadenylation of the resulting transcript. Transcription terminationsignals are generally found downstream of the polyadenylation signal andare a few hundred nucleotides in length. The term “poly A site” or “polyA sequence” as used herein denotes a DNA sequence that directs both thetermination and polyadenylation of the nascent RNA transcript. Efficientpolyadenylation of the recombinant transcript is desirable astranscripts lacking a poly A tail are unstable and are rapidly degraded.The poly A signal utilized in an expression vector may be “heterologous”or “endogenous.” An endogenous poly A signal is one that is foundnaturally at the 3′ end of the coding region of a given gene in thegenome. A heterologous poly A signal is one that is isolated from onegene and placed 3′ of another gene. A commonly used heterologous poly Asignal is the SV40 poly A signal. The SV40 poly A signal is contained ona 237 bp BamHI/BclI restriction fragment and directs both terminationand polyadenylation (Sambrook, supra, at 16.6-16.7).

Eukaryotic expression vectors may also contain “viral replicons” or“viral origins of replication.” Viral replicons are viral DNA sequencesthat allow for the extrachromosomal replication of a vector in a hostcell expressing the appropriate replication factors. Vectors thatcontain either the SV40 or polyoma virus origin of replication replicateto high “copy number” (up to 10⁴ copies/cell) in cells that express theappropriate viral T antigen. Vectors that contain the replicons frombovine papillomavirus or Epstein-Barr virus replicate extrachromosomallyat “low copy number” (˜100 copies/cell). However, it is not intendedthat expression vectors be limited to any particular viral origin ofreplication.

As used herein, the term “long terminal repeat” of “LTR” refers totranscriptional control elements located in or isolated from the U3region 5′ and 3′ of a retroviral genome. As is known in the art, longterminal repeats may be used as control elements in retroviral vectors,or isolated from the retroviral genome and used to control expressionfrom other types of vectors.

As used herein, the term “secretion signal” refers to any DNA sequencewhich when operably linked to a recombinant DNA sequence encodes asignal peptide which is capable of causing the secretion of therecombinant polypeptide. In general, the signal peptides comprise aseries of about 15 to 30 hydrophobic amino acid residues (See, e.g.,Zwizinski et al., J. Biol. Chem. 255(16): 7973-77 [1980], Gray et al.,Gene 39(2): 247-54 [1985], and Martial et al., Science 205: 602-607[1979]). Such secretion signal sequences are preferably derived fromgenes encoding polypeptides secreted from the cell type targeted fortissue-specific expression (e.g., secreted milk proteins for expressionin and secretion from mammary secretory cells). Secretory DNA sequences,however, are not limited to such sequences. Secretory DNA sequences fromproteins secreted from many cell types and organisms may also be used(e.g., the secretion signals for t-PA, serum albumin, lactoferrin, andgrowth hormone, and secretion signals from microbial genes encodingsecreted polypeptides such as from yeast, filamentous fungi, andbacteria).

As used herein, the terms “RNA export element” or “Pre-mRNA ProcessingEnhancer (PPE)” refer to 3′ and 5′ cis-acting post-transcriptionalregulatory elements that enhance export of RNA from the nucleus. “PPE”elements include, but are not limited to Mertz sequences (described inU.S. Pat. Nos. 5,914,267 and 5,686,120, all of which are incorporatedherein by reference) and woodchuck mRNA processing enhancer (WPRE;WO99/14310 and U.S. Pat. No. 6,136,597, each of which is incorporatedherein by reference).

As used herein, the term “polycistronic” refers to an mRNA encoding morethan polypeptide chain (See, e.g., WO 93/03143, WO 88/05486, andEuropean Pat. No. 117058, all of which are incorporated herein byreference). Likewise, the term “arranged in polycistronic sequence”refers to the arrangement of genes encoding two different polypeptidechains in a single mRNA.

As used herein, the term “internal ribosome entry site” or “IRES” refersto a sequence located between polycistronic genes that permits theproduction of the expression product originating from the second gene byinternal initiation of the translation of the dicistronic mRNA. Examplesof internal ribosome entry sites include, but are not limited to, thosederived from foot and mouth disease virus (FDV), encephalomyocarditisvirus, poliovirus and RDV (Scheper et al., Biochem. 76: 801-809 [1994];Meyer et al., J. Virol. 69: 2819-2824 [1995]; Jang et al., 1988, J.Virol. 62: 2636-2643 [1998]; Haller et al., J. Virol. 66: 5075-5086[1995]). Vectors incorporating IRES's may be assembled as is known inthe art. For example, a retroviral vector containing a polycistronicsequence may contain the following elements in operable association:nucleotide polylinker, gene of interest, an internal ribosome entry siteand a mammalian selectable marker or another gene of interest. Thepolycistronic cassette is situated within the retroviral vector betweenthe 5′ LTR and the 3′ LTR at a position such that transcription from the5′ LTR promoter transcribes the polycistronic message cassette. Thetranscription of the polycistronic message cassette may also be drivenby an internal promoter (e.g., cytomegalovirus promoter) or an induciblepromoter, which may be preferable depending on the use. Thepolycistronic message cassette can further comprise a cDNA or genomicDNA (gDNA) sequence operatively associated within the polylinker. Anymammalian selectable marker can be utilized as the polycistronic messagecassette mammalian selectable marker. Such mammalian selectable markersare well known to those of skill in the art and can include, but are notlimited to, kanamycin/G418, hygromycin B or mycophenolic acid resistancemarkers.

As used herein, the term “retrovirus” refers to a retroviral particlewhich is capable of entering a cell (i.e., the particle contains amembrane-associated protein such as an envelope protein or a viral Gglycoprotein which can bind to the host cell surface and facilitateentry of the viral particle into the cytoplasm of the host cell) andintegrating the retroviral genome (as a double-stranded provirus) intothe genome of the host cell. The term “retrovirus” encompassesOncovirinae (e.g., Moloney murine leukemia virus (MoMOLV), Moloneymurine sarcoma virus (MoMSV), and Mouse mammary tumor virus (MMTV),Spumavirinae, amd Lentivirinae (e.g., Human immunodeficiency virus,Simian immunodeficiency virus, Equine infection anemia virus, andCaprine arthritis-encephalitis virus; See, e.g., U.S. Pat. Nos.5,994,136 and 6,013,516, both of which are incorporated herein byreference).

As used herein, the term “retroviral vector” refers to a retrovirus thathas been modified to express a gene of interest. Retroviral vectors canbe used to transfer genes efficiently into host cells by exploiting theviral infectious process. Foreign or heterologous genes cloned (i.e.,inserted using molecular biological techniques) into the retroviralgenome can be delivered efficiently to host cells which are susceptibleto infection by the retrovirus. Through well known geneticmanipulations, the replicative capacity of the retroviral genome can bedestroyed. The resulting replication-defective vectors can be used tointroduce new genetic material to a cell but they are unable toreplicate. A helper virus or packaging cell line can be used to permitvector particle assembly and egress from the cell. Such retroviralvectors comprise a replication-deficient retroviral genome containing anucleic acid sequence encoding at least one gene of interest (i.e., apolycistronic nucleic acid sequence can encode more than one gene ofinterest), a 5′ retroviral long terminal repeat (5′ LTR); and a 3′retroviral long terminal repeat (3′ LTR).

The term “pseudotyped retroviral vector” refers to a retroviral vectorcontaining a heterologous membrane protein. The term“membrane-associated protein” refers to a protein (e.g., a viralenvelope glycoprotein or the G proteins of viruses in the Rhabdoviridaefamily such as VSV, Piry, Chandipura and Mokola) which are associatedwith the membrane surrounding a viral particle; thesemembrane-associated proteins mediate the entry of the viral particleinto the host cell. The membrane associated protein may bind to specificcell surface protein receptors, as is the case for retroviral envelopeproteins or the membrane-associated protein may interact with aphospholipid component of the plasma membrane of the host cell, as isthe case for the G proteins derived from members of the Rhabdoviridaefamily.

The term “heterologous membrane-associated protein” refers to amembrane-associated protein which is derived from a virus which is not amember of the same viral class or family as that from which thenucleocapsid protein of the vector particle is derived. “Viral class orfamily” refers to the taxonomic rank of class or family, as assigned bythe International Committee on Taxonomy of Viruses.

The term “Rhabdoviridae” refers to a family of enveloped RNA virusesthat infect animals, including humans, and plants. The Rhabdoviridaefamily encompasses the genus Vesiculovirus which includes vesicularstomatitis virus (VSV), Cocal virus, Piry virus, Chandipura virus, andSpring viremia of carp virus (sequences encoding the Spring viremia ofcarp virus are available under GenBank accession number U18101). The Gproteins of viruses in the Vesiculovirus genera are virally-encodedintegral membrane proteins that form externally projecting homotrimericspike glycoproteins complexes that are required for receptor binding andmembrane fusion. The G proteins of viruses in the Vesiculovirus generahave a covalently bound palmititic acid (C₁₆) moiety. The amino acidsequences of the G proteins from the Vesiculoviruses are fairly wellconserved. For example, the Piry virus G protein share about 38%identity and about 55% similarity with the VSV G proteins (severalstrains of VSV are known, e.g., Indiana, New Jersey, Orsay, San Juan,etc., and their G proteins are highly homologous). The Chandipura virusG protein and the VSV G proteins share about 37% identity and 52%similarity. Given the high degree of conservation (amino acid sequence)and the related functional characteristics (e.g., binding of the virusto the host cell and fusion of membranes, including syncytia formation)of the G proteins of the Vesiculoviruses, the G proteins from non-VSVVesiculoviruses may be used in place of the VSV G protein for thepseudotyping of viral particles. The G proteins of the Lyssa viruses(another genera within the Rhabdoviridae family) also share a fairdegree of conservation with the VSV G proteins and function in a similarmanner (e.g., mediate fusion of membranes) and therefore may be used inplace of the VSV G protein for the pseudotyping of viral particles. TheLyssa viruses include the Mokola virus and the Rabies viruses (severalstrains of Rabies virus are known and their G proteins have been clonedand sequenced). The Mokola virus G protein shares stretches of homology(particularly over the extracellular and transmembrane domains) with theVSV G proteins which show about 31% identity and 48% similarity with theVSV G proteins. Preferred G proteins share at least 25% identity,preferably at least 30% identity and most preferably at least 35%identity with the VSV G proteins. The VSV G protein from which NewJersey strain (the sequence of this G protein is provided in GenBankaccession numbers M27165 and M21557) is employed as the reference VSV Gprotein.

As used herein, the term “lentivirus vector” refers to retroviralvectors derived from the Lentiviridae family (e.g., humanimmunodeficiency virus, simian immunodeficiency virus, equine infectiousanemia virus, and caprine arthritis-encephalitis virus) that are capableof integrating into non-dividing cells (See, e.g., U.S. Pat. Nos.5,994,136 and 6,013,516, both of which are incorporated herein byreference).

The term “pseudotyped lentivirus vector” refers to lentivirus vectorcontaining a heterologous membrane protein (e.g., a viral envelopeglycoprotein or the G proteins of viruses in the Rhabdoviridae familysuch as VSV, Piry, Chandipura and Mokola).

As used herein, the term “transposon” refers to transposable elements(e.g., Tn5, Tn7, and TN10) that can move or transpose from one positionto another in a genome. In general, the transposition is controlled by atransposase. The term “transposon vector,” as used herein, refers to avector encoding a nucleic acid of interest flanked by the terminal endsof transposon. Examples of transposon vectors include, but are notlimited to, those described in U.S. Pat. Nos. 6,027,722; 5,958,775;5,968,785; 5,965,443; and 5,719,055, all of which are incorporatedherein by reference.

As used herein, the term “adeno-associated virus (AAV) vector” refers toa vector derived from an adeno-associated virus serotype, includingwithout limitation, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAVX7, etc. AAVvectors can have one or more of the AAV wild-type genes deleted in wholeor part, preferably the rep and/or cap genes, but retain functionalflanking ITR sequences.

AAV vectors can be constructed using recombinant techniques that areknown in the art to include one or more heterologous nucleotidesequences flanked on both ends (5′ and 3′) with functional AAV ITRs. Inthe practice of the invention, an AAV vector can include at least oneAAV ITR and a suitable promoter sequence positioned upstream of theheterologous nucleotide sequence and at least one AAV ITR positioneddownstream of the heterologous sequence. A “recombinant AAV vectorplasmid” refers to one type of recombinant AAV vector wherein the vectorcomprises a plasmid. As with AAV vectors in general, 5′ and 3′ ITRsflank the selected heterologous nucleotide sequence.

AAV vectors can also include transcription sequences such aspolyadenylation sites, as well as selectable markers or reporter genes,enhancer sequences, and other control elements which allow for theinduction of transcription. Such control elements are described above.

As used herein, the term “AAV virion” refers to a complete virusparticle. An AAV virion may be a wild type AAV virus particle(comprising a linear, single-stranded AAV nucleic acid genome associatedwith an AAV capsid, i.e., a protein coat), or a recombinant AAV virusparticle (described below). In this regard, single-stranded AAV nucleicacid molecules (either the sense/coding strand or theantisense/anticoding strand as those terms are generally defined) can bepackaged into an AAV virion; both the sense and the antisense strandsare equally infectious.

As used herein, the term “recombinant AAV virion” or “rAAV” is definedas an infectious, replication-defective virus composed of an AAV proteinshell encapsidating (i.e., surrounding with a protein coat) aheterologous nucleotide sequence, which in turn is flanked 5′ and 3′ byAAV ITRs. A number of techniques for constructing recombinant AAVvirions are known in the art (See, e.g., U.S. Pat. No. 5,173,414; WO92/01070; WO 93/03769; Lebkowski et al., Molec. Cell. Biol. 8:3988-3996[1988]; Vincent et al., Vaccines 90 [1990] (Cold Spring HarborLaboratory Press); Carter, Current Opinion in Biotechnology 3:533-539[1992]; Muzyczka, Current Topics in Microbiol. and Immunol. 158:97-129[1992]; Kotin, Human Gene Therapy 5:793-801 [1994]; Shelling and Smith,Gene Therapy 1:165-169 [1994]; and Zhou et al., J. Exp. Med.179:1867-1875 [1994], all of which are incorporated herein byreference).

Suitable nucleotide sequences for use in AAV vectors (and, indeed, anyof the vectors described herein) include any functionally relevantnucleotide sequence. Thus, the AAV vectors of the present invention cancomprise any desired gene that encodes a protein that is defective ormissing from a target cell genome or that encodes a non-native proteinhaving a desired biological or therapeutic effect (e.g., an antiviralfunction), or the sequence can correspond to a molecule having anantisense or ribozyme function. Suitable genes include those used forthe treatment of inflammatory diseases, autoimmune, chronic andinfectious diseases, including such disorders as AIDS, cancer,neurological diseases, cardiovascular disease, hypercholestemia; variousblood disorders including various anemias, thalasemias and hemophilia;genetic defects such as cystic fibrosis, Gaucher's Disease, adenosinedeaminase (ADA) deficiency, emphysema, etc. A number of antisenseoligonucleotides (e.g., short oligonucleotides complementary tosequences around the translational initiation site (AUG codon) of anmRNA) that are useful in antisense therapy for cancer and for viraldiseases have been described in the art. (See, e.g., Han et al., Proc.Natl. Acad. Sci. USA 88:4313-4317 [1991]; Uhlmann et al., Chem. Rev.90:543-584 [1990]; Helene et al., Biochim. Biophys. Acta. 1049:99-125[1990]; Agarwal et al., Proc. Natl. Acad. Sci. USA 85:7079-7083 [1989];and Heikkila et al., Nature 328:445-449 [1987]). For a discussion ofsuitable ribozymes, see, e.g., Cech et al. (1992) J. Biol. Chem.267:17479-17482 and U.S. Pat. No. 5,225,347, incorporated herein byreference.

By “adeno-associated virus inverted terminal repeats” or “AAV ITRs” ismeant the art-recognized palindromic regions found at each end of theAAV genome which function together in cis as origins of DNA replicationand as packaging signals for the virus. For use with the presentinvention, flanking AAV ITRs are positioned 5′ and 3′ of one or moreselected heterologous nucleotide sequences and, together with the repcoding region or the Rep expression product, provide for the integrationof the selected sequences into the genome of a target cell.

The nucleotide sequences of AAV ITR regions are known (See, e.g., Kotin,Human Gene Therapy 5:793-801 [1994]; Berns, K. I. “Parvoviridae andtheir Replication” in Fundamental Virology, 2nd Edition, (B. N. Fieldsand D. M. Knipe, eds.) for the AAV-2 sequence. As used herein, an “AAVITR” need not have the wild-type nucleotide sequence depicted, but maybe altered, e.g., by the insertion, deletion or substitution ofnucleotides. Additionally, the AAV ITR may be derived from any ofseveral AAV serotypes, including without limitation, AAV-1, AAV-2,AAV-3, AAV-4, AAV-5, AAVX7, etc. The 5′ and 3′ ITRs which flank aselected heterologous nucleotide sequence need not necessarily beidentical or derived from the same AAV serotype or isolate, so long asthey function as intended, i.e., to allow for the integration of theassociated heterologous sequence into the target cell genome when therep gene is present (either on the same or on a different vector), orwhen the Rep expression product is present in the target cell.

As used herein the term, the term “in vitro” refers to an artificialenvironment and to processes or reactions that occur within anartificial environment. In vitro environments can consist of, but arenot limited to, test tubes and cell cultures. The term “in vivo” refersto the natural environment (e.g., an animal or a cell) and to processesor reaction that occur within a natural environment.

As used herein, the term “clonally derived” refers to a cell line thatit derived from a single cell.

As used herein, the term “non-clonally derived” refers to a cell linethat is derived from more than one cell.

As used herein, the term “passage” refers to the process of diluting aculture of cells that has grown to a particular density or confluency(e.g., 70% or 80% confluent), and then allowing the diluted cells toregrow to the particular density or confluency desired (e.g., byreplating the cells or establishing a new roller bottle culture with thecells.

As used herein, the term “stable,” when used in reference to genome,refers to the stable maintenance of the information content of thegenome from one generation to the next, or, in the particular case of acell line, from one passage to the next. Accordingly, a genome isconsidered to be stable if no gross changes occur in the genome (e.g., agene is deleted or a chromosomal translocation occurs). The term“stable” does not exclude subtle changes that may occur to the genomesuch as point mutations.

As used herein, the term “response,” when used in reference to an assay,refers to the generation of a detectable signal (e.g., accumulation ofreporter protein, increase in ion concentration, accumulation of adetectable chemical product).

As used herein, the term “membrane receptor protein” refers to membranespanning proteins that bind a ligand (e.g., a hormone orneurotransmitter). As is known in the art, protein phosphorylation is acommon regulatory mechanism used by cells to selectively modify proteinscarrying regulatory signals from outside the cell to the nucleus. Theproteins that execute these biochemical modifications are a group ofenzymes known as protein kinases. They may further be defined by thesubstrate residue that they target for phosphorylation. One group ofprotein kinases are the tyrosine kinases (TKs) which selectivelyphosphorylate a target protein on its tyrosine residues. Some tyrosinekinases are membrane-bound receptors (RTKs), and, upon activation by aligand, can autophosphorylate as well as modify substrates. Theinitiation of sequential phosphorylation by ligand stimulation is aparadigm that underlies the action of such effectors as, for example,epidermal growth factor (EGF), insulin, platelet-derived growth factor(PDGF), and fibroblast growth factor (FGF). The receptors for theseligands are tyrosine kinases and provide the interface between thebinding of a ligand (hormone, growth factor) to a target cell and thetransmission of a signal into the cell by the activation of one or morebiochemical pathways. Ligand binding to a receptor tyrosine kinaseactivates its intrinsic enzymatic activity (See, e.g., Ullrich andSchlessinger, Cell 61:203-212 [1990]). Tyrosine kinases can also becytoplasmic, non-receptor-type enzymes and act as a downstream componentof a signal transduction pathway.

As used herein, the term “signal transduction protein” refers to aproteins that are activated or otherwise effected by ligand binding to amembrane receptor protein or some other stimulus. Examples of signaltransduction protein include adenyl cyclase, phospholipase C, andG-proteins. Many membrane receptor proteins are coupled to G-proteins(i.e., G-protein coupled receptors (GPCRs); for a review, see Neer,1995, Cell 80:249-257 [1995]). Typically, GPCRs contain seventransmembrane domains. Putative GPCRs can be identified on the basis ofsequence homology to known GPCRs.

GPCRs mediate signal transduction across a cell membrane upon thebinding of a ligand to an extracellular portion of a GPCR. Theintracellular portion of a GPCR interacts with a G-protein to modulatesignal transduction from outside to inside a cell. A GPCR is thereforesaid to be “coupled” to a G-protein. G-proteins are composed of threepolypeptide subunits: an α subunit, which binds and hydrolyses GTP, anda dimeric βγ subunit. In the basal, inactive state, the G-protein existsas a heterotrimer of the α and βγ subunits. When the G-protein isinactive, guanosine diphosphate (GDP) is associated with the α subunitof the G-protein. When a GPCR is bound and activated by a ligand, theGPCR binds to the G-protein heterotrimer and decreases the affinity ofthe Gα subunit for GDP. In its active state, the G subunit exchanges GDPfor guanine triphosphate (GTP) and active Gα subunit disassociates fromboth the receptor and the dimeric βγ subunit. The disassociated, activeGα subunit transduces signals to effectors that are “downstream” in theG-protein signalling pathway within the cell. Eventually, theG-protein's endogenous GTPase activity returns active G subunit to itsinactive state, in which it is associated with GDP and the dimeric βγsubunit.

Numerous members of the heterotrimeric G-protein family have beencloned, including more than 20 genes encoding various Gα subunits. Thevarious G subunits have been categorized into four families, on thebasis of amino acid sequences and functional homology. These fourfamilies are termed Gα_(s), Gα_(i), Gα_(q), and Gα₁₂. Functionally,these four families differ with respect to the intracellular signalingpathways that they activate and the GPCR to which they couple.

For example, certain GPCRs normally couple with Gα_(s) and, throughGα_(s), these GPCRs stimulate adenylyl cyclase activity. Other GPCRsnormally couple with GGα_(q), and through GGα_(q), these GPCRs canactivate phospholipase C(PLC), such as the β isoform of phospholipase C(i.e., PLCβ, Stermweis and Smrcka, Trends in Biochem. Sci. 17:502-506[1992]).

As used herein, the term “nucleic acid binding protein” refers toproteins that bind to nucleic acid, and in particular to proteins thatcause increased (i.e., activators or transcription factors) or decreased(i.e., inhibitors) transcription from a gene.

As used herein, the term “ion channel protein” refers to proteins thatcontrol the ingress or egress of ions across cell membranes. Examples ofion channel proteins include, but are not limited to, the Na⁺-K⁺ ATPasepump, the Ca²⁺ pump, and the K⁺ leak channel.

As used herein, the term “protein kinase” refers to proteins thatcatalyze the addition of a phosphate group from a nucleosidetriphosphate to an amino acid side chain in a protein. Kinases comprisethe largest known enzyme superfamily and vary widely in their targetproteins. Kinases may be categorized as protein tyrosine kinases (PTKs),which phosphorylate tyrosine residues, and protein serine/threoninekinases (STKs), which phosphorylate serine and/or threonine residues.Some kinases have dual specificity for both serine/threonine andtyrosine residues. Almost all kinases contain a conserved 250-300 aminoacid catalytic domain. This domain can be further divided into 11subdomains. N-terminal subdomains I-IV fold into a two-lobed structurewhich binds and orients the ATP donor molecule, and subdomain V spansthe two lobes. C-terminal subdomains VI-XI bind the protein substrateand transfer the gamma phosphate from ATP to the hydroxyl group of aserine, threonine, or tyrosine residue. Each of the 11 subdomainscontains specific catalytic residues or amino acid motifs characteristicof that subdomain. For example, subdomain I contains an 8-amino acidglycine-rich ATP binding consensus motif, subdomain II contains acritical lysine residue required for maximal catalytic activity, andsubdomains VI through IX comprise the highly conserved catalytic core.STKs and PTKs also contain distinct sequence motifs in subdomains VI andVIII which may confer hydroxyamino acid specificity. Some STKs and PTKspossess structural characteristics of both families. In addition,kinases may also be classified by additional amino acid sequences,generally between 5 and 100 residues, which either flank or occur withinthe kinase domain.

Non-transmembrane PTKs form signaling complexes with the cytosolicdomains of plasma membrane receptors. Receptors that signal throughnon-transmembrane PTKs include cytokine, hormone, and antigen-specificlymphocytic receptors. Many PTKs were first identified as oncogeneproducts in cancer cells in which PTK activation was no longer subjectto normal cellular controls. In fact, about one third of the knownoncogenes encode PTKs. Furthermore, cellular transformation(oncogenesis) is often accompanied by increased tyrosine phosphorylationactivity (See, e.g., Carbonneau, H. and Tonks, Annu. Rev. Cell Biol.8:463-93 [1992]). Regulation of PTK activity may therefore be animportant strategy in controlling some types of cancer.

Examples of protein kinases include, but are not limited to,cAMP-dependent protein kinase, protein kinase C, and cyclin-dependentprotein kinases (See, e.g., U.S. Pat. Nos. 6,034,228; 6,030,822;6,030,788; 6,020,306; 6,013,455; 6,013,464; and 6,015,807, all of whichare incorporated herein by reference).

As used herein, the term “protein phosphatase” refers to proteins thatremove a phosphate group from a protein. Protein phosphatases aregenerally divided into two groups, receptor and non-receptor typeproteins. Most receptor-type protein tyrosine phosphatases contain twoconserved catalytic domains, each of which encompasses a segment of 240amino acid residues. (See, e.g., Saito et al., Cell Growth and Diff.2:59-65 [1991]). Receptor protein tyrosine phosphatases can besubclassified further based upon the amino acid sequence diversity oftheir extracellular domains. (See, e.g., Krueger et al., Proc. Natl.Acad. Sci. USA 89:7417-7421 [1992]). Examples of protein phosphatasesinclude, but are not limited to, cdc25 a, b, and c, PTP20, PTP1D, andPTPλ (See, e.g., U.S. Pat. Nos. 5,976,853; 5,994,074; 6,004,791;5,981,251; 5,976,852; 5,958,719; 5,955,592; and 5,952,212, all of whichare incorporated herein by reference).

As used herein, the term “protein encoded by an oncogene” refers toproteins that cause, either directly or indirectly, the neoplastictransformation of a host cell. Examples of oncogenes include, but arenot limited to, the following genes: src, fps, fes, fgr, ros, H-ras,abl, ski, erbA, erbB, fms, fos, mos, sis, myc, myb, rel kit, raf, K-ras,and ets.

As used herein, the term “immunoglobulin” refers to proteins which binda specific antigen. Immunoglobulins include, but are not limited to,polyclonal, monoclonal, chimeric, and humanized antibodies, Fabfragments, F(ab′)2 fragments, and includes immunoglobulins of thefollowing classes: IgG, IgA, IgM, IgD, IbE, and secreted immunoglobulins(sIg). Immunoglobulins generally comprise two identical heavy chains (γ,α, μ, δ, or ε) and two light chains (κ or λ).

As used herein, the term “antigen binding protein” refers to proteinswhich bind to a specific antigen. “Antigen binding proteins” include,but are not limited to, immunoglobulins, including polyclonal,monoclonal, chimeric, and humanized antibodies; Fab fragments, F(ab′)2fragments, and Fab expression libraries; and single chain antibodies.Various procedures known in the art are used for the production ofpolyclonal antibodies. For the production of an antibody, various hostanimals can be immunized by injection with the peptide corresponding tothe desired epitope including but not limited to rabbits, mice, rats,sheep, goats, etc. In a preferred embodiment, the peptide is conjugatedto an immunogenic carrier (e.g., diphtheria toxoid, bovine serum albumin(BSA), or keyhole limpet hemocyanin (KLH)). Various adjuvants are usedto increase the immunological response, depending on the host species,including but not limited to Freund's (complete and incomplete), mineralgels such as aluminum hydroxide, surface active substances such aslysolecithin, pluronic polyols, polyanions, peptides, oil emulsions,keyhole limpet hemocyanins, dinitrophenol, and potentially useful humanadjuvants such as BCG (Bacille Calmette-Guerin) and Corynebacteriumparvum.

For preparation of monoclonal antibodies, any technique that providesfor the production of antibody molecules by continuous cell lines inculture may be used (See, e.g., Harlow and Lane, Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y.). These include, but are not limited to, the hybridomatechnique originally developed by Köhler and Milstein (Köhler andMilstein, Nature 256:495-497 [1975]), as well as the trioma technique,the human B-cell hybridoma technique (See e.g., Kozbor et al. Immunol.Today 4:72 [1983]), and the EBV-hybridoma technique to produce humanmonoclonal antibodies (Cole et al., in Monoclonal Antibodies and CancerTherapy, Alan R. Liss, Inc., pp. 77-96 [1985]).

According to the invention, techniques described for the production ofsingle chain antibodies (U.S. Pat. No. 4,946,778; herein incorporated byreference) can be adapted to produce specific single chain antibodies asdesired. An additional embodiment of the invention utilizes thetechniques known in the art for the construction of Fab expressionlibraries (Huse et al., Science 246:1275-1281 [1989]) to allow rapid andeasy identification of monoclonal Fab fragments with the desiredspecificity.

Antibody fragments that contain the idiotype (antigen binding region) ofthe antibody molecule can be generated by known techniques. For example,such fragments include but are not limited to: the F(ab′)2 fragment thatcan be produced by pepsin digestion of an antibody molecule; the Fab′fragments that can be generated by reducing the disulfide bridges of anF(ab′)2 fragment, and the Fab fragments that can be generated bytreating an antibody molecule with papain and a reducing agent.

Genes encoding antigen binding proteins can be isolated by methods knownin the art. In the production of antibodies, screening for the desiredantibody can be accomplished by techniques known in the art (e.g.,radioimmunoassay, ELISA (enzyme-linked immunosorbant assay), “sandwich”immunoassays, immunoradiometric assays, gel diffusion precipitinreactions, immunodiffusion assays, in situ immunoassays (using colloidalgold, enzyme or radioisotope labels, for example), Western Blots,precipitation reactions, agglutination assays (e.g., gel agglutinationassays, hemagglutination assays, etc.), complement fixation assays,immunofluorescence assays, protein A assays, and immunoelectrophoresisassays, etc.) etc.

As used herein, the term “reporter gene” refers to a gene encoding aprotein that may be assayed. Examples of reporter genes include, but arenot limited to, luciferase (See, e.g., deWet et al., Mol. Cell. Biol.7:725 [1987] and U.S. Pat. Nos. 6,074,859; 5,976,796; 5,674,713; and5,618,682; all of which are incorporated herein by reference), greenfluorescent protein (e.g., GenBank Accession Number U43284; a number ofGFP variants are commercially available from CLONTECH Laboratories, PaloAlto, Calif.), chloramphenicol acetyltransferase, β-galactosidase,alkaline phosphatase, and horse radish peroxidase.

As used herein, the term “purified” refers to molecules, either nucleicor amino acid sequences, that are removed from their naturalenvironment, isolated or separated. An “isolated nucleic acid sequence”is therefore a purified nucleic acid sequence. “Substantially purified”molecules are at least 60% free, preferably at least 75% free, and morepreferably at least 90% free from other components with which they arenaturally associated.

The term “test compound” refers to any chemical entity, pharmaceutical,drug, and the like contemplated to be useful in the treatment and/orprevention of a disease, illness, sickness, or disorder of bodilyfunction, or otherwise alter the physiological or cellular status of asample. Test compounds comprise both known and potential therapeuticcompounds. A test compound can be determined to be therapeutic byscreening using the screening methods of the present invention. A “knowntherapeutic compound” refers to a therapeutic compound that has beenshown (e.g., through animal trials or prior experience withadministration to humans) to be effective in such treatment orprevention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to the production of proteins in hostcells, and more particularly to host cells containing multipleintegrated copies of an integrating vector. The present inventionutilizes integrating vectors (i.e., vectors that integrate via anintegrase or transposase) to create cell lines containing a high copynumber of a nucleic acid encoding a gene of interest. The transfectedgenomes of the high copy number cells are stable through repeatedpassages (e.g., at least 10 passages, preferably at least 50 passages,and most preferably at least 100 passages). Furthermore, the host cellsof the present invention are capable of producing high levels of protein(e.g., more than 1 pg/cell/day, preferably more than 10 pg/cell/day,more preferably more than 50 pg/cell/day, and most preferably more than100 pg/cell/day.)

The genomic stability and high expression levels of the host cells ofthe present invention provide distinct advantages over previouslydescribed methods of cell culture. For example, mammalian cell linescontaining multiple copies of genes are known in the art to beintrinsically unstable. Indeed, this instability is a recognized problemfacing researchers desiring to use mammalian cell lines for variouspurposes, including high throughput screening assays (See, e.g.,Sittampalam et al., Curr. Opin. Chem. Biol. 1(3):384-91 [1997]).

It is not intended that the present invention be limited to particularmechanism of action. Indeed, an understanding of the mechanism is notnecessary to make and use the present invention. However, the highgenomic stability and protein expression levels of the host cells of thepresent invention are thought to be due to unique properties of theintegrating vectors (e.g., retroviral vectors). For example, it is knownthat retroviruses are inherited elements in the germ line of manyorganisms. Indeed, as much as 5-10% of the mammalian genome may consistof elements contributed by reverse transcription, indicating a highdegree of stability. Likewise, many of these types of vectors targetactive (e.g., DNase I hypersensitive sites) transcriptional sites in thegenome.

Many investigations have focused on the deleterious effects ofretroviral and transposon integration. The property of targeting activeregions of the genome has led to the use of retroviral vectors andtransposon vectors in promoter trap schemes and for saturationmutagenesis (See, e.g., U.S. Pat. Nos. 5,627,058 and 5,922,601, all ofwhich are herein incorporated by reference). In promoter trap schemes,the cells are infected with a promoterless reporter vector. If thepromoterless vector integrates downstream of a promoter (i.e., into agene), the reporter gene encoded by the vector is activated. Thepromoter can then be cloned and further characterized.

As can be seen, these schemes rely on the disruption of an endogenousgene. Therefore, it is surprising that the methods of the presentinvention, which utilize integrating vectors at high multiplicities ofinfection that would normally be thought to lead to gene disruption, ledto the development of stable cell lines that express high quantities ofa protein of interest. The development of these cell lines is describedmore fully below. The description is divided into the followingsections: I) Host Cells; II) Vectors and Methods of Transfection; andIII) Uses of Transfected Host Cells.

I. Host Cells

The present invention contemplates the transfection of a variety of hostcells with integrating vectors. A number of mammalian host cell linesare known in the art. In general, these host cells are capable of growthand survival when placed in either monolayer culture or in suspensionculture in a medium containing the appropriate nutrients and growthfactors, as is described in more detail below. Typically, the cells arecapable of expressing and secreting large quantities of a particularprotein of interest into the culture medium. Examples of suitablemammalian host cells include, but are not limited to Chinese hamsterovary cells (CHO-K1, ATCC CCl-61); bovine mammary epithelial cells (ATCCCRL 10274; bovine mammary epithelial cells); monkey kidney CV1 linetransformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line(293 or 293 cells subcloned for growth in suspension culture; see, e.g.,Graham et al., J. Gen Virol., 36:59 [1977]); baby hamster kidney cells(BHK, ATCC CCL 10); mouse sertoli cells (TM4, Mather, Biol. Reprod.23:243-251 [1980]); monkey kidney cells (CV1 ATCC CCL 70); African greenmonkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinomacells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34);buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138,ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor(MMT 060562, ATCC CCL51); TR1 cells (Mather et al., Annals N.Y. Acad.Sci., 383:44-68 [1982]); MRC 5 cells; FS4 cells; rat fibroblasts (208Fcells); MDBK cells (bovine kidney cells); and a human hepatoma line (HepG2).

In addition to mammalian cell lines, the present invention alsocontemplates the transfection of plant protoplasts with integratingvectors at a low or high multiplicity of infection. For example, thepresent invention contemplates a plant cell or whole plant comprising atleast one integrated integrating vector, preferably a retroviral vector,and most preferably a pseudotyped retroviral vector. All plants that canbe produced by regeneration from protoplasts can also be transfectedusing the process according to the invention (e.g., cultivated plants ofthe genera Solanum, Nicotiana, Brassica, Beta, Pisum, Phaseolus,Glycine, Helianthus, Allium, Avena, Hordeum, Oryzae, Setaria, Secale,Sorghum, Triticum, Zea, Musa, Cocos, Cydonia, Pyrus, Malus, Phoenix,Elaeis, Rubus, Fragaria, Prunus, Arachis, Panicum, Saccharum, Coffea,Camellia, Ananas, Vitis or Citrus). In general, protoplasts are producedin accordance with conventional methods (See, e.g., U.S. Pat. Nos.4,743,548; 4,677,066, 5,149,645; and 5,508,184; all of which areincorporated herein by reference). Plant tissue may be dispersed in anappropriate medium having an appropriate osmotic potential (e.g., 3 to 8wt. % of a sugar polyol) and one or more polysaccharide hydrolases(e.g., pectinase, cellulase, etc.), and the cell wall degradationallowed to proceed for a sufficient time to provide protoplasts. Afterfiltration the protoplasts may be isolated by centrifugation and maythen be resuspended for subsequent treatment or use. Regeneration ofprotoplasts kept in culture to whole plants is performed by methodsknown in the art (See, e.g., Evans et al., Handbook of Plant CellCulture, 1: 124-176, MacMillan Publishing Co., New York [1983]; Binding,Plant Protoplasts, p. 21-37, CRC Press, Boca Raton [1985],) and Potrykusand Shillito, Methods in Enzymology, Vol. 118, Plant Molecular Biology,A. and H. Weissbach eds., Academic Press, Orlando [1986]).

The present invention also contemplates the use of amphibian and insecthost cell lines. Examples of suitable insect host cell lines include,but are not limited to, mosquito cell lines (e.g., ATCC CRL-1660).Examples of suitable amphibian host cell lines include, but are notlimited to, toad cell lines (e.g., ATCC CCL-102).

II. Vectors and Methods for Transfection

According to the present invention, host cells such as those describedabove are transduced or transfected with integrating vectors. Examplesof integrating vectors include, but are not limited to, retroviralvectors, lentiviral vectors, adeno-associated viral vectors, andtransposon vectors. The design, production, and use of these vectors inthe present invention is described below.

A. Retroviral Vectors

Retroviruses (family Retroviridae) are divided into three groups: thespumaviruses (e.g., human foamy virus); the lentiviruses (e.g., humanimmunodeficiency virus and sheep visna virus) and the oncoviruses (e.g.,MLV, Rous sarcoma virus).

Retroviruses are enveloped (i.e., surrounded by a host cell-derivedlipid bilayer membrane) single-stranded RNA viruses which infect animalcells. When a retrovirus infects a cell, its RNA genome is convertedinto a double-stranded linear DNA form (i.e., it is reversetranscribed). The DNA form of the virus is then integrated into the hostcell genome as a provirus. The provirus serves as a template for theproduction of additional viral genomes and viral mRNAs. Mature viralparticles containing two copies of genomic RNA bud from the surface ofthe infected cell. The viral particle comprises the genomic RNA, reversetranscriptase and other pol gene products inside the viral capsid (whichcontains the viral gag gene products) which is surrounded by a lipidbilayer membrane derived from the host cell containing the viralenvelope glycoproteins (also referred to as membrane-associatedproteins).

The organization of the genomes of numerous retroviruses is well knownto the art and this has allowed the adaptation of the retroviral genometo produce retroviral vectors. The production of a recombinantretroviral vector carrying a gene of interest is typically achieved intwo stages.

First, the gene of interest is inserted into a retroviral vector whichcontains the sequences necessary for the efficient expression of thegene of interest (including promoter and/or enhancer elements which maybe provided by the viral long terminal repeats (LTRs) or by an internalpromoter/enhancer and relevant splicing signals), sequences required forthe efficient packaging of the viral RNA into infectious virions (e.g.,the packaging signal (Psi), the tRNA primer binding site (−PBS), the 3′regulatory sequences required for reverse transcription (+PBS)) and theviral LTRs. The LTPs contain sequences required for the association ofviral genomic RNA, reverse transcriptase and integrase functions, andsequences involved in directing the expression of the genomic RNA to bepackaged in viral particles. For safety reasons, many recombinantretroviral vectors lack functional copies of the genes which areessential for viral replication (these essential genes are eitherdeleted or disabled); therefore, the resulting virus is said to bereplication defective.

Second, following the construction of the recombinant vector, the vectorDNA is introduced into a packaging cell line. Packaging cell linesprovide proteins required in trans for the packaging of the viralgenomic RNA into viral particles having the desired host range (i.e.,the viral-encoded gag, pol and env proteins). The host range iscontrolled, in part, by the type of envelope gene product expressed onthe surface of the viral particle. Packaging cell lines may expressecotrophic, amphotropic or xenotropic envelope gene products.Alternatively, the packaging cell line may lack sequences encoding aviral envelope (env) protein. In this case the packaging cell line willpackage the viral genome into particles which lack a membrane-associatedprotein (e.g., an env protein). In order to produce viral particlescontaining a membrane associated protein which will permit entry of thevirus into a cell, the packaging cell line containing the retroviralsequences is transfected with sequences encoding a membrane-associatedprotein (e.g., the G protein of vesicular stomatitis virus (VSV)). Thetransfected packaging cell will then produce viral particles whichcontain the membrane-associated protein expressed by the transfectedpackaging cell line; these viral particles which contain viral genomicRNA derived from one virus encapsidated by the envelope proteins ofanother virus are said to be pseudotyped virus particles.

The retroviral vectors of the present invention can be further modifiedto include additional regulatory sequences. As described above, theretroviral vectors of the present invention include the followingelements in operable association: a) a 5′ LTR; b) a packaging signal; c)a 3′ LTR and d) a nucleic acid encoding a protein of interest locatedbetween the 5′ and 3′ LTRs. In some embodiments of the presentinvention, the nucleic acid of interest may be arranged in oppositeorientation to the 5′ LTR when transcription from an internal promoteris desired. Suitable internal promoters include, but are not limited to,the alpha-lactalbumin promoter, the CMV promoter (human or ape), and thethymidine kinase promoter.

In other embodiments of the present invention, where secretion of theprotein of interest is desired, the vectors are modified by including asignal peptide sequence in operable association with the protein ofinterest. The sequences of several suitable signal peptides are known tothose in the art, including, but not limited to, those derived fromtissue plasminogen activator, human growth hormone, lactoferrin,alpha-casein, and alpha-lactalbumin.

In other embodiments of the present invention, the vectors are modifiedby incorporating an RNA export element (See, e.g., U.S. Pat. Nos.5,914,267; 6,136,597; and 5,686,120; and WO99/14310, all of which areincorporated herein by reference) either 3′ or 5′ to the nucleic acidsequence encoding the protein of interest. It is contemplated that theuse of RNA export elements allows high levels of expression of theprotein of interest without incorporating splice signals or introns inthe nucleic acid sequence encoding the protein of interest.

In still other embodiments, the vector further comprises at least oneinternal ribosome entry site (IRES) sequence. The sequences of severalsuitable IRES's are available, including, but not limited to, thosederived from foot and mouth disease virus (FDV), encephalomyocarditisvirus, and poliovirus. The IRES sequence can be interposed between twotranscriptional units (e.g., nucleic acids encoding different proteinsof interest or subunits of a multisubunit protein such as an antibody)to form a polycistronic sequence so that the two transcriptional unitsare transcribed from the same promoter.

The retroviral vectors of the present invention may also furthercomprise a selectable marker allowing selection of transformed cells. Anumber of selectable markers find use in the present invention,including, but not limited to the bacterial aminoglycoside 3′phosphotransferase gene (also referred to as the neo gene) that confersresistance to the drug G418 in mammalian cells, the bacterial hygromycinG phosphotransferase (hyg) gene that confers resistance to theantibiotic hygromycin and the bacterial xanthine-guanine phosphoribosyltransferase gene (also referred to as the gpt gene) that confers theability to grow in the presence of mycophenolic acid. In someembodiments, the selectable marker gene is provided as part ofpolycistronic sequence that also encodes the protein of interest.

In still other embodiments of the present invention, the retroviralvectors may comprise recombination elements recognized by arecombination system (e.g., the cre/loxP or flp recombinase systems,see, e.g., Hoess et al., Nucleic Acids Res. 14:2287-2300 [1986],O'Gorman et al., Science 251:1351-55 [1991], van Deursen et al., Proc.Natl. Acad. Sci. USA 92:7376-80 [1995], and U.S. Pat. No. 6,025,192,herein incorporated by reference). After integration of the vectors intothe genome of the host cell, the host cell can be transientlytransfected (e.g., by electroporation, lipofection, or microinjection)with either a recombinase enzyme (e.g., Cre recombinase) or a nucleicacid sequence encoding the recombinase enzyme and one or more nucleicacid sequences encoding a protein of interest flanked by sequencesrecognized by the recombination enzyme so that the nucleic acid sequenceis inserted into the integrated vector.

Viral vectors, including recombinant retroviral vectors, provide a moreefficient means of transferring genes into cells as compared to othertechniques such as calcium phosphate-DNA co-precipitation orDEAE-dextran-mediated transfection, electroporation or microinjection ofnucleic acids. It is believed that the efficiency of viral transfer isdue in part to the fact that the transfer of nucleic acid is areceptor-mediated process (i.e., the virus binds to a specific receptorprotein on the surface of the cell to be infected). In addition, thevirally transferred nucleic acid once inside a cell integrates incontrolled manner in contrast to the integration of nucleic acids whichare not virally transferred; nucleic acids transferred by other meanssuch as calcium phosphate-DNA co-precipitation are subject torearrangement and degradation.

The most commonly used recombinant retroviral vectors are derived fromthe amphotropic Moloney murine leukemia virus (MoMLV) (See e.g., Millerand Baltimore Mol. Cell. Biol. 6:2895 [1986]). The MoMLV system hasseveral advantages: 1) this specific retrovirus can infect manydifferent cell types, 2) established packaging cell lines are availablefor the production of recombinant MoMLV viral particles and 3) thetransferred genes are permanently integrated into the target cellchromosome. The established MoMLV vector systems comprise a DNA vectorcontaining a small portion of the retroviral sequence (e.g., the virallong terminal repeat or “LTR” and the packaging or “psi” signal) and apackaging cell line. The gene to be transferred is inserted into the DNAvector. The viral sequences present on the DNA vector provide thesignals necessary for the insertion or packaging of the vector RNA intothe viral particle and for the expression of the inserted gene. Thepackaging cell line provides the proteins required for particle assembly(Markowitz et al., J. Virol. 62:1120 [1988]).

Despite these advantages, existing retroviral vectors based upon MoMLVare limited by several intrinsic problems: 1) they do not infectnon-dividing cells (Miller et al., Mol. Cell. Biol. 10:4239 [1990]),except, perhaps, oocytes; 2) they produce low titers of the recombinantvirus (Miller and Rosman, BioTechniques 7: 980 [1980] and Miller, Nature357: 455 [1990]); and 3) they infect certain cell types (e.g., humanlymphocytes) with low efficiency (Adams et al., Proc. Natl. Acad. Sci.USA 89:8981 [1992]). The low titers associated with MoMLV-based vectorshave been attributed, at least in part, to the instability of thevirus-encoded envelope protein. Concentration of retrovirus stocks byphysical means (e.g., ultracentrifugation and ultrafiltration) leads toa severe loss of infectious virus.

The low titer and inefficient infection of certain cell types byMoMLV-based vectors has been overcome by the use of pseudotypedretroviral vectors which contain the G protein of VSV as the membraneassociated protein. Unlike retroviral envelope proteins which bind to aspecific cell surface protein receptor to gain entry into a cell, theVSV G protein interacts with a phospholipid component of the plasmamembrane (Mastromarino et al., J. Gen. Virol. 68:2359 [1977]). Becauseentry of VSV into a cell is not dependent upon the presence of specificprotein receptors, VSV has an extremely broad host range. Pseudotypedretroviral vectors bearing the VSV G protein have an altered host rangecharacteristic of VSV (i.e., they can infect almost all species ofvertebrate, invertebrate and insect cells). Importantly, VSVG-pseudotyped retroviral vectors can be concentrated 2000-fold or moreby ultracentrifugation without significant loss of infectivity (Burns etal. Proc. Natl. Acad. Sci. USA 90:8033 [1993]).

The present invention is not limited to the use of the VSV G proteinwhen a viral G protein is employed as the heterologousmembrane-associated protein within a viral particle (See, e.g., U.S.Pat. No. 5,512,421, which is incorporated herein by reference). The Gproteins of viruses in the Vesiculovirus genera other than VSV, such asthe Piry and Chandipura viruses, that are highly homologous to the VSV Gprotein and, like the VSV G protein, contain covalently linked palmiticacid (Brun et al. Intervirol. 38:274 [1995] and Masters et al., Virol.171:285 (1990]). Thus, the G protein of the Piry and Chandipura virusescan be used in place of the VSV G protein for the pseudotyping of viralparticles. In addition, the VSV G proteins of viruses within the Lyssavirus genera such as Rabies and Mokola viruses show a high degree ofconservation (amino acid sequence as well as functional conservation)with the VSV G proteins. For example, the Mokola virus G protein hasbeen shown to function in a manner similar to the VSV G protein (i.e.,to mediate membrane fusion) and therefore may be used in place of theVSV G protein for the pseudotyping of viral particles (Mebatsion et al.,J. Virol. 69:1444 [1995]). Viral particles may be pseudotyped usingeither the Piry, Chandipura or Mokola G protein as described in Example2, with the exception that a plasmid containing sequences encodingeither the Piry, Chandipura or Mokola G protein under thetranscriptional control of a suitable promoter element (e.g., the CMVintermediate-early promoter; numerous expression vectors containing theCMV IE promoter are available, such as the pcDNA3.1 vectors(Invitrogen)) is used in place of pHCMV-G. Sequences encoding other Gproteins derived from other members of the Rhabdoviridae family may beused; sequences encoding numerous rhabdoviral G proteins are availablefrom the GenBank database.

The majority of retroviruses can transfer or integrate a double-strandedlinear form of the virus (the provirus) into the genome of the recipientcell only if the recipient cell is cycling (i.e., dividing) at the timeof infection. Retroviruses which have been shown to infect dividingcells exclusively, or more efficiently, include MLV, spleen necrosisvirus, Rous sarcoma virus and human immunodeficiency virus (HIV; whileHIV infects dividing cells more efficiently, HIV can infect non-dividingcells).

It has been shown that the integration of MLV virus DNA depends upon thehost cell's progression through mitosis and it has been postulated thatthe dependence upon mitosis reflects a requirement for the breakdown ofthe nuclear envelope in order for the viral integration complex to gainentry into the nucleus (Roe et al., EMBO J. 12:2099 [1993]). However, asintegration does not occur in cells arrested in metaphase, the breakdownof the nuclear envelope alone may not be sufficient to permit viralintegration; there may be additional requirements such as the state ofcondensation of the genomic DNA (Roe et al., supra).

B. Lentiviral Vectors

The present invention also contemplates the use of lentiviral vectors togenerate high copy number cell lines. The lentiviruses (e.g., equineinfectious anemia virus, caprine arthritis-encephalitis virus, humanimmunodeficiency virus) are a subfamily of retroviruses that are able tointegrate into non-dividing cells. The lentiviral genome and theproviral DNA have the three genes found in all retroviruses: gag, pol,and env, which are flanked by two LTR sequences. The gag gene encodesthe internal structural proteins (e.g., matrix, capsid, and nucleocapsidproteins); the pol gene encodes the reverse transcriptase, protease, andintegrase proteins; and the pol gene encodes the viral envelopeglycoproteins. The 5′ and 3′ LTRs control transcription andpolyadenylation of the viral RNAs. Additional genes in the lentiviralgenome include the vif, vpr, tat, rev, vpu, nef, and vpx genes.

A variety of lentiviral vectors and packaging cell lines are known inthe art and find use in the present invention (See, e.g., U.S. Pat. Nos.5,994,136 and 6,013,516, both of which are herein incorporated byreference). Furthermore, the VSV G protein has also been used topseudotype retroviral vectors based upon the human immunodeficiencyvirus (HIV) (Naldini et al., Science 272:263 [1996]). Thus, the VSV Gprotein may be used to generate a variety of pseudotyped retroviralvectors and is not limited to vectors based on MoMLV. The lentiviralvectors may also be modified as described above to contain variousregulatory sequences (e.g., signal peptide sequences, RNA exportelements, and IRES's). After the lentiviral vectors are produced, theymay be used to transfect host cells as described above for retroviralvectors.

C. Adeno-Associated Viral Vectors

The present invention also contemplates the use of adeno associatedvirus (AAV) vectors to generate high copy number cell lines. AAV is ahuman DNA parvovirus which belongs to the genus Dependovirus. The AAVgenome is composed of a linear, single-stranded DNA molecule whichcontains approximately 4680 bases. The genome includes inverted terminalrepeats (ITRs) at each end which function in cis as origins of DNAreplication and as packaging signals for the virus. The internalnonrepeated portion of the genome includes two large open readingframes, known as the AAV rep and cap regions, respectively. Theseregions code for the viral proteins involved in replication andpackaging of the virion. A family of at least four viral proteins aresynthesized from the AAV rep region, Rep 78, Rep 68, Rep 52 and Rep 40,named according to their apparent molecular weight. The AAV cap regionencodes at least three proteins, VP1, VP2 and VP3 (for a detaileddescription of the AAV genome, see e.g., Muzyczka, Current TopicsMicrobiol. Immunol. 158:97-129 [1992]; Kotin, Human Gene Therapy5:793-801 [1994]).

AAV requires coinfection with an unrelated helper virus, such asadenovirus, a herpesvirus or vaccinia, in order for a productiveinfection to occur. In the absence of such coinfection, AAV establishesa latent state by insertion of its genome into a host cell chromosome.Subsequent infection by a helper virus rescues the integrated copy whichcan then replicate to produce infectious viral progeny. Unlike thenon-pseudotyped retroviruses, AAV has a wide host range and is able toreplicate in cells from any species so long as there is coinfection witha helper virus that will also multiply in that species. Thus, forexample, human AAV will replicate in canine cells coinfected with acanine adenovirus. Furthermore, unlike the retroviruses, AAV is notassociated with any human or animal disease, does not appear to alterthe biological properties of the host cell upon integration and is ableto integrate into nondividing cells. It has also recently been foundthat AAV is capable of site-specific integration into a host cellgenome.

In light of the above-described properties, a number of recombinant AAVvectors have been developed for gene delivery (See, e.g., U.S. Pat. Nos.5,173,414; 5,139,941; WO 92/01070 and WO 93/03769, both of which areincorporated herein by reference; Lebkowski et al., Molec. Cell. Biol.8:3988-3996 [1988]; Carter, B. J., Current Opinion in Biotechnology3:533-539 [1992]; Muzyczka, Current Topics in Microbiol. and Immunol.158:97-129 [1992]; Kotin, R. M. (1994) Human Gene Therapy 5:793-801;Shelling and Smith, Gene Therapy 1:165-169 [1994]; and Zhou et al., J.Exp. Med. 179:1867-1875 [1994]).

Recombinant AAV virions can be produced in a suitable host cell whichhas been transfected with both an AAV helper plasmid and an AAV vector.An AAV helper plasmid generally includes AAV rep and cap coding regions,but lacks AAV ITRs. Accordingly, the helper plasmid can neitherreplicate nor package itself. An AAV vector generally includes aselected gene of interest bounded by AAV ITRs which provide for viralreplication and packaging functions. Both the helper plasmid and the AAVvector bearing the selected gene are introduced into a suitable hostcell by transient transfection. The transfected cell is then infectedwith a helper virus, such as an adenovirus, which transactivates the AAVpromoters present on the helper plasmid that direct the transcriptionand translation of AAV rep and cap regions. Recombinant AAV virionsharboring the selected gene are formed and can be purified from thepreparation. Once the AAV vectors are produced, they may be used totransfect (See, e.g., U.S. Pat. No. 5,843,742, herein incorporated byreference) host cells at the desired multiplicity of infection toproduce high copy number host cells. As will be understood by thoseskilled in the art, the AAV vectors may also be modified as describedabove to contain various regulatory sequences (e.g., signal peptidesequences, RNA export elements, and IRES's).

D. Transposon Vectors

The present invention also contemplates the use of transposon vectors togenerate high copy number cell lines. Transposons are mobile geneticelements that can move or transpose from one location another in thegenome. Transposition within the genome is controlled by a transposaseenzyme that is encoded by the transposon. Many examples of transposonsare known in the art, including, but not limited to, Tn5 (See e.g., dela Cruz et al., J. Bact. 175: 6932-38 [1993], Tn7 (See e.g., Craig,Curr. Topics Microbiol. Immunol. 204: 27-48 [1996]), and Tn10 (See e.g.,Morisato and Kleckner, Cell 51:101-111 [1987]). The ability oftransposons to integrate into genomes has been utilized to createtransposon vectors (See, e.g., U.S. Pat. Nos. 5,719,055; 5,968,785;5,958,775; and 6,027,722; all of which are incorporated herein byreference.) Because transposons are not infectious, transposon vectorsare introduced into host cells via methods known in the art (e.g.,electroporation, lipofection, or microinjection). Therefore, the ratioof transposon vectors to host cells may be adjusted to provide thedesired multiplicity of infection to produce the high copy number hostcells of the present invention.

Transposon vectors suitable for use in the present invention generallycomprise a nucleic acid encoding a protein of interest interposedbetween two transposon insertion sequences. Some vectors also comprise anucleic acid sequence encoding a transposase enzyme. In these vectors,the one of the insertion sequences is positioned between the transposaseenzyme and the nucleic acid encoding the protein of interest so that itis not incorporated into the genome of the host cell duringrecombination. Alternatively, the transposase enzyme may be provided bya suitable method (e.g., lipofection or microinjection). As will beunderstood by those skilled in the art, the transposon vectors may alsobe modified as described above to contain various regulatory sequences(e.g., signal peptide sequences, RNA export elements, and IRES's).

E. Transfection at High Multiplicities of Infection

Once integrating vectors (e.g., retroviral vectors) encoding a proteinof interest have been produced, they may be used to transfect ortransduce host cells (examples of which are described above in SectionI). Preferably, host cells are transfected or transduced withintegrating vectors at a multiplicity of infection sufficient to resultin the integration of at least 1, and preferably at least 2 or moreretroviral vectors. In some embodiments, multiplicities of infection offrom 10 to 1,000,000 may be utilized, so that the genomes of theinfected host cells contain from 2 to 100 copies of the integratedvectors, and preferably from 5 to 50 copies of the integrated vectors.In other embodiments, a multiplicity of infection of from 10 to 10,000is utilized. When non-pseudotyped retroviral vectors are utilized forinfection, the host cells are incubated with the culture medium from theretroviral producers cells containing the desired titer (i.e., colonyforming units, CFUs) of infectious vectors. When pseudotyped retroviralvectors are utilized, the vectors are concentrated to the appropriatetiter by ultracentrifugation and then added to the host cell culture.Alternatively, the concentrated vectors can be diluted in a culturemedium appropriate for the cell type. Additionally, when expression ofmore than one protein of interest by the host cell is desired, the hostcells can be transfected with multiple vectors each containing a nucleicacid encoding a different protein of interest.

In each case, the host cells are exposed to medium containing theinfectious retroviral vectors for a sufficient period of time to allowinfection and subsequent integration of the vectors. In general, theamount of medium used to overlay the cells should be kept to as small avolume as possible so as to encourage the maximum amount of integrationevents per cell. As a general guideline, the number of colony formingunits (cfu) per milliliter should be about 10⁵ to 10⁷ cfu/ml, dependingupon the number of integration events desired.

The present invention is not limited to any particular mechanism ofaction. Indeed, an understanding of the mechanism of action is notnecessary for practicing the present invention. However, the diffusionrate of the vectors is known to be very limited (See, e.g., U.S. Pat.No. 5,866,400, herein incorporated by reference, for a discussion ofdiffusion rates). Therefore, it is expected that the actual integrationrate will be lower (and in some cases much lower) than the multiplicityof infection. Applying the equations from U.S. Pat. No. 5,866,400, atiter of 10⁶ cfu/ml has an average vector-vector spacing of 1 micron.The diffusion time of a MMLV vector across 100 microns is approximately20 minutes. Accordingly, the vector can travel approximately 300 micronsin one hour. If 1000 cells are plated in a T25 flask, the cells arespaced 2.5 mm apart on average. Using these values, the only 56 viralparticles would be expected to contact a given cell within an hour. TheTable below provides the expected contact rate for a given number ofcells in a T25 flask with a particular vector titer. However, as shownbelow in the examples, the actual number of integrations obtained ismuch lower than may be predicted by these equations.

Vector Contact Frequency As A Function of Time and Cell Spacing VectorTiter Cells/T25 Flask MOI Contacts/Hour 10⁶ 1000 1,000 56 10⁶ 100 10,000<56 10⁵ 1000 100 5.6 10⁴ 1000 10 0.6

Accordingly, it is contemplated that the actual integration rate isdependent not only on the multiplicity of infection, but also on thecontact time (i.e., the length of time the host cells are exposed toinfectious vector), the confluency or geometry of the host cells beingtransfected, and the volume of media that the vectors are contained in.It is contemplated that these conditions can be varied as taught hereinto produce host cell lines containing multiple integrated copies ofintegrating vectors. As demonstrated in Examples 8 and 9, MOI can bevaried by either holding the number of cells constant and varying CFU's(Example 9), or by holding CFU's constant and varying cell number(Example 8).

In some embodiments, after transfection or transduction, the cells areallowed to multiply, and are then trypsinized and replated. Individualcolonies are then selected to provide clonally selected cell lines. Instill further embodiments, the clonally selected cell lines are screenedby Southern blotting or INVADER assay to verify that the desired numberof integration events has occurred. It is also contemplated that clonalselection allows the identification of superior protein producing celllines. In other embodiments, the cells are not clonally selectedfollowing transfection.

In some embodiments, the host cells are transfected with vectorsencoding different proteins of interest. The vectors encoding differentproteins of interest can be used to transfect the cells at the same time(e.g., the host cells are exposed to a solution containing vectorsencoding different proteins of interest) or the transfection can beserial (e.g., the host cells are first transfected with a vectorencoding a first protein of interest, a period of time is allowed topass, and the host cells are then transfected with a vector encoding asecond protein of interest). In some preferred embodiments, the hostcells are transfected with an integrating vector encoding a firstprotein of interest, high expressing cell lines containing multipleintegrated copies of the integrating vector are selected (e.g., clonallyselected), and the selected cell line is transfected with an integratingvector encoding a second protein of interest. This process may berepeated to introduce multiple proteins of interest. In someembodiments, the multiplicities of infection may be manipulated (e.g.,increased or decreased) to increase or decrease the expression of theprotein of interest. Likewise, the different promoters may be utilizedto vary the expression of the proteins of interest. It is contemplatedthat these transfection methods can be used to construct host cell linescontaining an entire exogenous metabolic pathway or to provide hostcells with an increased capability to process proteins (e.g., the hostcells can be provided with enzymes necessary for post-translationalmodification).

In still further embodiments, cell lines are serially transfected withvectors encoding the same gene. In some preferred embodiments, the hostcells are transfected (e.g., at an MOI of about 10 to 100,000,preferably 100 to 10,000) with an integrating vector encoding a proteinof interest, cell lines containing single or multiple integrated copiesof the integrating vector or expressing high levels of the desiredprotein are selected (e.g., clonally selected), and the selected cellline is retransfected with the vector (e.g., at an MOI of about 10 to100,000, preferably 100 to 10,000). In some embodiments, cell linescomprising at least two integrated copies of the vector are identifiedand selected. This process may be repeated multiple times until thedesired level of protein expression is obtained and may also be repeatedto introduce vectors encoding multiple proteins of interest.Unexpectedly, serial transfection with the same gene results inincreases in protein production from the resulting cells that are notmerely additive.

III. Uses of Transfected Host Cells

The host cells transfected at a high multiplicity of infection can beused for a variety of purposes. First, the host cells find use in theproduction of proteins for pharmaceutical, industrial, diagnostic, andother purposes. Second, host cells expressing a particular protein orproteins find use in screening assays (e.g., high throughput screening).Third, the host cells find use in the production of multiple variants ofproteins, followed by analysis of the activity of the protein variants.Each of these uses is explained in more detail below.

A. Production of Proteins

It is contemplated that the host cells of the present invention find usein the production of proteins for pharmaceutical, industrial,diagnostic, and other uses. The present invention is not limited to theproduction of any particular protein. Indeed, the production of a widevariety of proteins is contemplated, including, but not limited to,erythropoietin, alpha-interferon, alpha-1 proteinase inhibitor,angiogenin, antithrombin III, beta-acid decarboxylase, human growthhormone, bovine growth hormone, porcine growth hormone, human serumalbumin, beta-interferon, calf intestine alkaline phosphatase, cysticfibrosis transmembrane regulator, Factor VIII, Factor IX, Factor X,insulin, lactoferrin, tissue plasminogen activator, myelin basicprotein, insulin, proinsulin, prolactin, hepatitis B antigen,immunoglobulins, monoclonal antibody CTLA4 Ig, Tag 72 monoclonalantibody, Tag 72 single chain antigen binding protein, protein C,cytokines and their receptors, including, for instance tumor necrosisfactors alpha and beta, their receptors and their derivatives; renin;growth hormone releasing factor; parathyroid hormone; thyroidstimulating hormone; lipoproteins; alpha-1-antitrypsin; folliclestimulating hormone; calcitonin; luteinizing hormone; glucagon; vonWillebrands factor; atrial natriuretic factor; lung surfactant;urokinase; bombesin; thrombin; hemopoietic growth factor; enkephalinase;human macrophage inflammatory protein (MIP-1-alpha); a serum albuminsuch mullerian-inhibiting substance; relaxin A-chain; relaxin B-chain;prorelaxin; mouse gonadotropin-associated peptide; beta-lactamase;DNase; inhibin; activin; vascular endothelial growth factor (VEGF);receptors for hormones or growth factors; integrin; protein A or D;rheumatoid factors; a neurotrophic factor such as bone-derivedneurotrophic factor (BDNF), neurotrophin-3, -4, -5, or -6 (NT-3, NT-4,NT-5, or NT-6), or a nerve growth factor such as NGF-beta;platelet-derived growth factor (PDGF); fibroblast growth factor such asaFGF and bFGF; epidermal growth factor (EGF); transforming growth factor(TGF) such as TGF-alpha and TGF-beta, including TGF-β1, TGF-β2, TGF-β3,TGF-β4, or TGF-β5; insulin-like growth factor-I and -II (IGF-I andIGF-II); des(1-3)-IGF-I (brain IGF-I), insulinslike growth factorbinding proteins; CD proteins such as CD-3, CD-4, CD-8, and CD-19;osteoinductive factors; immunotoxins; a bone morphogenetic protein(BMP); an interferon such as interferon-alpha, -beta, and -gamma; colonystimulating factors (CSFs), e.g., M-CSF, GM-CSF, and G-CSF; interleukins(ILs), e.g., IL-1 to IL-10; superoxide dismutase; T-cell receptors;surface membrane proteins; decay accelerating factor; viral antigen suchas, for example, a portion of the AIDS envelope; transport proteins;homing receptors; addressins; regulatory proteins; antibodies; chimericproteins, such as immunoadhesins, and fragments of any of theabove-listed polypeptides. Nucleic acid and protein sequences for theseproteins are available in public databases such as GenBank.

In some embodiments, the host cells express more than one exogenousprotein. For example, the host cells may be transfected vectors encodingdifferent proteins of interest (e.g., cotransfection or infection at amultiplicity of infection of 1000 with one vector encoding a firstprotein of interest and a second vector encoding a second protein ofinterest or serial transfection or infection) so that the host cellcontains at least one integrated copy of a first vector encoding a firstprotein of interest and at least one integrated copy of secondintegrating vector encoding a second protein of interest. In otherembodiments, more than one protein is expressed by arranging the nucleicacids encoding the different proteins of interest in a polycistronicsequence (e.g., bicistronic or tricistronic sequences). This arrangementis especially useful when expression of the different proteins ofinterest in about a 1:1 molar ratio is desired (e.g., expressing thelight and heavy chains of an antibody molecule).

In still further embodiments, ribozymes are expressed in the host cells.It is contemplated that the ribozyme can be utilized for down-regulatingexpression of a particular gene or used in conjunction with geneswitches such as TET, ecdysone, glucocorticoid enhancer, etc. to providehost cells with various phenotypes.

The transfected host cells are cultured according to methods known inthe art.

Suitable culture conditions for mammalian cells are well known in theart (See e.g., J. Immunol. Methods (1983) 56:221-234 [1983], Animal CellCulture: A Practical Approach 2nd Ed., Rickwood, D. and Hames, B. D.,eds. Oxford University Press, New York [1992]).

The host cell cultures of the present invention are prepared in a mediasuitable for the particular cell being cultured. Commercially availablemedia such as Ham's F10 (Sigma, St. Louis, Mo.), Minimal EssentialMedium (MEM, Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle'sMedium (DMEM, Sigma) are exemplary nutrient solutions. Suitable mediaare also described in U.S. Pat. Nos. 4,767,704; 4,657,866; 4,927,762;5,122,469; 4,560,655; and WO 90/03430 and WO 87/00195; the disclosuresof which are herein incorporated by reference. Any of these media may besupplemented as necessary with serum, hormones and/or other growthfactors (such as insulin, transferrin, or epidermal growth factor),salts (such as sodium chloride, calcium, magnesium, and phosphate),buffers (such as HEPES), nucleosides (such as adenosine and thymidine),antibiotics (such as gentamycin (gentarnicin), trace elements (definedas inorganic compounds usually present at final concentrations in themicromolar range) lipids (such as linoleic or other fatty acids) andtheir suitable carriers, and glucose or an equivalent energy source. Anyother necessary supplements may also be included at appropriateconcentrations that would be known to those skilled in the art. Formammalian cell culture, the osmolality of the culture medium isgenerally about 290-330 mOsm.

The present invention also contemplates the use of a variety of culturesystems (e.g., petri dishes, 96 well plates, roller bottles, andbioreactors) for the transfected host cells. For example, thetransfected host cells can be cultured in a perfusion system. Perfusionculture refers to providing a continuous flow of culture medium througha culture maintained at high cell density. The cells are suspended anddo not require a solid support to grow on. Generally, fresh nutrientsmust be supplied continuously with concomitant removal of toxicmetabolites and, ideally, selective removal of dead cells. Filtering,entrapment and micro-capsulation methods are all suitable for refreshingthe culture environment at sufficient rates.

As another example, in some embodiments a fed batch culture procedurecan be employed. In the preferred fed batch culture the mammalian host,cells and culture medium are supplied to a culturing vessel initiallyand additional culture nutrients are fed, continuously or in discreteincrements, to the culture during culturing, with or without periodiccell and/or product harvest before termination of culture. The fed batchculture can include, for example, a semi-continuous fed batch culture,wherein periodically whole culture (including cells and medium) isremoved and replaced by fresh medium. Fed batch culture is distinguishedfrom simple batch culture in which all components for cell culturing(including the cells and all culture nutrients) are supplied to theculturing vessel at the start of the culturing process. Fed batchculture can be further distinguished from perfusion culturing insofar asthe supernate is not removed from the culturing vessel during theprocess (in perfusion culturing, the cells are restrained in the cultureby, e.g., filtration, encapsulation, anchoring to microcarriers etc. andthe culture medium is continuously or intermittently introduced andremoved from the culturing vessel). In some particularly preferredembodiments, the batch cultures are performed in roller bottles.

Further, the cells of the culture may be propagated according to anyscheme or routine that may be suitable for the particular host cell andthe particular production plan contemplated. Therefore, the presentinvention contemplates a single step or multiple step culture procedure.In a single step culture the host cells are inoculated into a cultureenvironment and the processes of the instant invention are employedduring a single production phase of the cell culture. Alternatively, amulti-stage culture is envisioned. In the multi-stage culture cells maybe cultivated in a number of steps or phases. For instance, cells may begrown in a first step or growth phase culture wherein cells, possiblyremoved from storage, are inoculated into a medium suitable forpromoting growth and high viability. The cells may be maintained in thegrowth phase for a suitable period of time by the addition of freshmedium to the host cell culture.

Fed batch or continuous cell culture conditions are devised to enhancegrowth of the mammalian cells in the growth phase of the cell culture.In the growth phase cells are grown under conditions and for a period oftime that is maximized for growth. Culture conditions, such astemperature, pH, dissolved oxygen (dO₂) and the like, are those usedwith the particular host and will be apparent to the ordinarily skilledartisan. Generally, the pH is adjusted to a level between about 6.5 and7.5 using either an acid (e.g., CO₂) or a base (e.g., Na₂CO₃ or NaOH). Asuitable temperature range for culturing mammalian cells such as CHOcells is between about 30° to 38° C. and a suitable dO₂ is between 5-90%of air saturation.

Following the polypeptide production phase, the polypeptide of interestis recovered from the culture medium using techniques which are wellestablished in the art. The protein of interest preferably is recoveredfrom the culture medium as a secreted polypeptide (e.g., the secretionof the protein of interest is directed by a signal peptide sequence),although it also may be recovered from host cell lysates. As a firststep, the culture medium or lysate is centrifuged to remove particulatecell debris. The polypeptide thereafter is purified from contaminantsoluble proteins and polypeptides, with the following procedures beingexemplary of suitable purification procedures: by fractionation onimmunoaffinity or ion-exchange columns; ethanol precipitation; reversephase HPLC; chromatography on silica or on a cation-exchange resin suchas DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gelfiltration using, for example, Sephadex G-75; and protein A Sepharosecolumns to remove contaminants such as IgG. A protease inhibitor such asphenyl methyl sulfonyl fluoride (PMSF) also may be useful to inhibitproteolytic degradation during purification. Additionally, the proteinof interest can be fused in frame to a marker sequence which allows forpurification of the protein of interest. Non-limiting examples of markersequences include a hexahistidine tag which may be supplied by a vector,preferably a pQE-9 vector, and a hemagglutinin (HA) tag. The HA tagcorresponds to an epitope derived from the influenza hemagglutininprotein (See e.g., Wilson et al., Cell, 37:767 [1984]). One skilled inthe art will appreciate that purification methods suitable for thepolypeptide of interest may require modification to account for changesin the character of the polypeptide upon expression in recombinant cellculture.

The host cells of the present invention are also useful for expressingG-protein coupled receptors (GPCRs) and other transmembrane proteins. Itis contemplated that when these proteins are expressed, they arecorrectly inserted into the membrane in their native conformation. Thus,GPCRs and other transmembrane proteins may be purified as part of amembrane fraction or purified from the membranes by methods known in theart.

Furthermore, the vectors of the present invention are useful forco-expressing a protein of interest for which there is no assay or forwhich assays are difficult. In this system, a protein of interest and asignal protein are arranged in a polycistronic sequence. Preferably, anIRES sequence separates the signal protein and protein of interest(e.g., a GPCR) and the genes encoding the signal protein and protein ofinterest are expressed as a single transcriptional unit. The presentinvention is not limited to any particular signal protein. Indeed, theuse of a variety of signal proteins for which easy assays exist iscontemplated. These signal proteins include, but are not limited to,green fluorescent protein, luciferase, beta-galactosidase, and antibodyheavy or light chains. It is contemplated that when the signal proteinand protein of interest are co-expressed from a polycistronic sequence,the presence of the signal protein is indicative of the presence of theprotein of interest. Accordingly, in some embodiments, the presentinvention provides methods for indirectly detecting the expression of aprotein of interest comprising providing a host cell transfected with avector encoding a polycistronic sequence, wherein the polycistronicsequence comprises a signal protein and a protein of interest operablylinked by an IRES, and culturing the host cells under conditions suchthat the signal protein and protein of interest are produced, whereinthe presence of the signal protein indicates the presence of the proteinof interest.

B. Screening Compounds for Activity

The present invention contemplates the use of the high copy number celllines for screening compounds for activity, and in particular to highthroughput screening of compounds from combinatorial libraries (e.g.,libraries containing greater than 10⁴ compounds). The high copy numbercell lines of the present invention can be used in a variety ofscreening methods. In some embodiments, the cells can be used in secondmessenger assays that monitor signal transduction following activationof cell-surface receptors. In other embodiments, the cells can be usedin reporter gene assays that monitor cellular responses at thetranscription/translation level. In still further embodiments, the cellscan be used in cell proliferation assays to monitor the overallgrowth/no growth response of cells to external stimuli.

In second messenger assays, the host cells are preferably transfected asdescribed above with vectors encoding cell surface receptors, ionchannels, cytoplasmic receptors, or other proteins involved in signaltransduction (e.g., G proteins, protein kinases, or proteinphosphatases) (See, e.g., U.S. Pat. Nos. 5,670,113; 5,807,689;5,876,946; and 6,027,875; all of which are incorporated herein byreference). The host cells are then treated with a compound or pluralityof compounds (e.g., from a combinatorial library) and assayed for thepresence or absence of a response. It is contemplated that at least someof the compounds in the combinatorial library can serve as agonists,antagonists, activators, or inhibitors of the protein or proteinsencoded by the vectors. It is also contemplated that at least some ofthe compounds in the combinatorial library can serve as agonists,antagonists, activators, or inhibitors of protein acting upstream ordownstream of the protein encoded by the vector in a signal transductionpathway.

By way of non-limiting example, it is known that agonist engagedtransmembrane receptors are functionally linked to the modulation ofseveral well characterized promoter/enhancer elements (e.g., AP1, cAMPresponse element (CRE), serum response element (SRE), and nuclear factorof activated T-cells (NF-AT)). Upon activation of a G_(αs) couplingreceptor, adenylyl cyclase is stimulated, producing increasedconcentrations of intracellular cAMP, stimulation of protein kinase A,phosphorylation of the CRE binding protein (CREB) and induction ofpromoters with CRE elements. G_(αi) coupling receptors dampen CREactivity by inhibition of the same signal transduction components.G_(αq) and some βγ pairs stimulate phospholipase C(PLC), and thegeneration of inositol triphosphate (IP3) and diacylglycerol (DAG). Atransient flux in intracellular calcium promotes induction ofcalcineurin and NA-FT, as well as calmodulin (CaM)-dependent kinase andCREB. Increased DAG concentrations stimulate protein kinase C(PKC) andendosomal/lysosomal acidic sphingomyelinase (aSMase); while the aSMasepathway is dominant, both induce degradation of the NFκB inhibitor IκBas well as NFκB activation. In an alternative pathway, a receptor suchas growth factor receptor is activated and recruits Sos to the plasmamembrane, resulting in the stimulation of Ras, which in turn recruitsthe serine/threonine kinase Raf to the plasma membrane. Once activated,Raf phosphorylates MEK kinase, which phosphorylates and activates MAPKand the transcription factor ELK. ELK drives transcription frompromoters with SRE elements, leading the synthesis of the transcriptionfactors Fos and Jun, thus forming a transcription factor complex capableof activating AP1 sites. It is contemplated that the proteins formingthe described pathways, as well as other receptors, kinases,phosphatases, and nucleic binding proteins, are targets for compounds inthe combinatorial library, as well as candidates for expression in thehost cells of the present invention.

In some embodiments, the second messenger assays measure fluorescentsignals from reporter molecules that respond to intracellular changes(e.g., Ca²⁺ concentration, membrane potential, pH, IP₃, cAMP,arachidonic acid release) due to stimulation of membrane receptors andion channels (e.g., ligand gated ion channels; see Denyer et al., DrugDiscov. Today 3:323-32 [1998]; and Gonzales et al., Drug. Discov. Today4:431-39 [1999]). Examples of reporter molecules include, but are notlimited to, FRET (florescence resonance energy transfer) systems (e.g.,Cuo-lipids and oxonols, EDAN/DABCYL), calcium sensitive indicators(e.g., Fluo-3, FURA 2, INDO 1, and FLUO3 μM, BAPTA AM),chloride-sensitive indicators (e.g., SPQ, SPA), potassium-sensitiveindicators (e.g., PBFI), sodium-sensitive indicators (e.g., SBFI), andpH sensitive indicators (e.g., BCECF).

In general, the host cells are loaded with the indicator prior toexposure to the compound. Responses of the host cells to treatment withthe compounds can be detected by methods known in the art, including,but not limited to, fluorescence microscopy, confocal microscopy (e.g.,FCS systems), flow cytometry, microfluidic devices, FLIPR systems (See,e.g., Schroeder and Neagle, J. Biomol. Screening 1:75-80 [1996]), andplate-reading systems. In some preferred embodiments, the response(e.g., increase in fluorescent intensity) caused by compound of unknownactivity is compared to the response generated by a known agonist andexpressed as a percentage of the maximal response of the known agonist.The maximum response caused by a known agonist is defined as a 100%response. Likewise, the maximal response recorded after addition of anagonist to a sample containing a known or test antagonist is detectablylower than the 100% response.

The cells are also useful in reporter gene assays. Reporter gene assaysinvolve the use of host cells transfected with vectors encoding anucleic acid comprising transcriptional control elements of a targetgene (i.e., a gene that controls the biological expression and functionof a disease target) spliced to a coding sequence for a reporter gene.Therefore, activation of the target gene results in activation of thereporter gene product. Examples of reporter genes finding use in thepresent invention include, but are not limited to, chloramphenicoltransferase, alkaline phosphatase, firefly and bacterial luciferases,α-galactosidase, β-lactamase, and green fluorescent protein. Theproduction of these proteins, with the exception of green fluorescentprotein, is detected through the use of chemiluminescent, calorimetric,or bioluminecent products of specific substrates (e.g., X-gal andluciferin). Comparsions between compounds of known and unknownactivities may be conducted as described above.

C. Comparison of Variant Protein Activity

The present invention also contemplates the use of the high copy numberhost cells to produce variants of proteins so that the activity of thevariants can be compared. In some embodiments, the variants differ by asingle nucleotide polymorphism (SNP) causing a single amino aciddifference. In other embodiments, the variants contain multiple aminoacid substitutions. In some embodiments, the activity of the variantproteins are assayed in vivo or in cell extracts. In other embodiments,the proteins are purified and assayed in vitro. It is also contemplatedthat in some embodiments the variant proteins are fused to a sequencethat allows easy purification (e.g., a his-tag sequence) or to areporter gene (e.g., green fluorescent protein). Activity of theproteins may be assayed by appropriate methods known in the art (e.g.,conversion of a substrate to a product). In some preferred embodiments,the activity of a wild-type protein is determined, and the activity ofvariant versions of the wild-type proteins are expressed as a percentageof the activity of the wild-type protein. Furthermore, the intracellularactivity of variant proteins may be compared by constructing a pluralityof host cells lines, each of which expresses a different variant of thewild-type protein. The activity of the variant proteins (e.g., variantsof proteins involved in signal transduction pathways) may then becompared using the reporter systems for second messenger assaysdescribed above. Therefore, in some embodiments, the direct or indirectresponse (e.g., through downstream or upstream activation of signaltransduction pathway) of variant proteins to stimulation or binding byagonists or antagonists is compared. In some preferred embodiments, theresponse of a wild-type protein is determined, and the responses ofvariant versions of the wild-type proteins are expressed as a percentageof the response of the wild-type protein.

Experimental

The following examples serve to illustrate certain preferred embodimentsand aspects of the present invention and are not to be construed aslimiting the scope thereof.

In the experimental disclosure which follows, the followingabbreviations apply: M (molar); mM (millimolar); μM (micromolar); nM(nanomolar); mol (moles); mmol (millimoles); μmol (micromoles); nmol(nanomoles); gm (grams); mg (milligrams); μg (micrograms); pg(picograms); L (liters); ml (milliliters); μl (microliters); cm(centimeters); mm (millimeters); μm (micrometers); nm (nanometers); ° C.(degrees Centigrade); AMP (adenosine 5′-monophosphate); BSA (bovineserum albumin); cDNA (copy or complimentary DNA); CS (calf serum); DNA(deoxyribonucleic acid); ssDNA (single stranded DNA); dsDNA (doublestranded DNA); dNTP (deoxyribonucleotide triphosphate); LH (luteinizinghormone); NIH (National Institues of Health, Besthesda, Md.); RNA(ribonucleic acid); PBS (phosphate buffered saline); g (gravity); OD(optical density); HEPES(N-[2-Hydroxyethyl]piperazine-N-[2-ethanesulfonic acid]); HBS (HEPESbuffered saline); PBS (phosphate buffered saline); SDS (sodiumdodecylsulfate); Tris.HCl(tris[Hydroxymethyl]aminomethane-hydrochloride); Klenow (DNA polymeraseI large (Klenow) fragment); rpm (revolutions per minute); EGTA (ethyleneglycol-bis(β-aminoethyl ether) N,N, N′,N′-tetraacetic acid); EDTA(ethylenediaminetetracetic acid); bla (β-lactamase orampicillin-resistance gene); OR1 (plasmid origin of replication); lacI(lac repressor); X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactoside);ATCC (American Type Culture Collection, Rockville, Md.); GIBCO/BRL(GIBCO/BRL, Grand Island, N.Y.); Perkin-Elmer (Perkin-Elmer, Norwalk,Conn.); and Sigma (Sigma Chemical Company, St. Louis, Mo.).

EXAMPLE 1 Vector Construction

The following Example describes the construction of vectors used in theexperiments below.

A. CMV MN14

The CMV MN14 vector (SEQ ID NO:4; MN14 antibody is described in U.S.Pat. No. 5,874,540, incorporated herein by reference) comprises thefollowing elements, arranged in 5′ to 3′ order: CMV promoter; MN14 heavychain signal peptide, MN14 antibody heavy chain; IRES fromencephalomyocarditis virus; bovine α-lactalbumin signal peptide; MN14antibody light chain; and 3′ MoMuLV LTR. In addition to sequencesdescribed in SEQ ID NO: 4, the CMV MN14 vector further comprises a 5′MoMuLV LTR, a MoMuLV extended viral packaging signal, and a neomycinphosphotransferase gene (these additional elements are provided in SEQID NO:7; the 5′ LTR is derived from Moloney Murine Sarcoma Virus in eachof the constructs described herein, but is converted to the MoMuLV 5′LTR when integrated).

This construct uses the 5′ MoMuLV LTR to control production of theneomycin phosphotransferase gene. The expression of MN14 antibody iscontrolled by the CMV promoter. The MN14 heavy chain gene and lightchain gene are attached together by an IRES sequence. The CMV promoterdrives production of a mRNA containing the heavy chain gene and thelight chain gene attached by the IRES. Ribosomes attach to the mRNA atthe CAP site and at the IRES sequence. This allows both heavy and lightchain protein to be produced from a single mRNA. The mRNA expressionfrom the LTR as well as from the CMV promoter is terminated and polyadenylated in the 3′ LTR. The construct was cloned by similar methods asdescribed in section B below.

The IRES sequence (SEQ ID NO:3) comprises a fusion of the IRES from theplasmid pLXIN (Clontech) and the bovine α-lactalbumin signal peptide.The initial ATG of the signal peptide was attached to the IRES to allowthe most efficient translation initiation from the IRES. The 3′ end ofthe signal peptide provides a multiple cloning site allowing easyattachment of any protein of interest to create a fusion protein withthe signal peptide. The IRES sequence can serve as a translationalenhancer as well as creating a second translation initiation site thatallows two proteins to be produced from a single mRNA.

The IRES-bovine α-lactalbumin signal peptide was constructed as follows.The portion of the plasmid pLXIN (Clontech, Palo Alto, Calif.)containing the ECMV IRES was PCR amplified using the following primers.

Primer 1 (SEQ ID NO: 35): 5′ GATCCACTAGTAACGGCCGCCAGAATTCGC 3′ Primer 2(SEQ ID NO: 36): 5′ CAGAGAGACAAAGGAGGCCATATTATCATCGTGTTTTTCAAAG 3′

Primer 2 attaches a tail corresponding to the start of the bovineα-lactalbumin signal peptide coding region to the IRES sequence. Inaddition, the second triplet codon of the α-lactalbumin signal peptidewas mutated from ATG to GCC to allow efficient translation from the IRESsequence. This mutation results in a methionine to alanine change in theprotein sequence. This mutation was performed because the IRES prefersan alanine as the second amino acid in the protein chain. The resultingIRES PCR product contains an EcoRI site on the 5′ end of the fragment((just downstream of Primer 1 above).

Next, the α-lactalbumin signal peptide containing sequence was PCRamplified from the α-LA Signal Peptide vector construct using thefollowing primers.

Primer 3 (SEQ ID NO: 14): 5′ CTTTGAAAAACACGATGATAATATGGCCTCCTTTGTCTCTCTG3′ Primer 4 (SEQ ID NO: 15): 5′ TTCGCGAGCTCGAGATCTAGATATCCCATG 3′

Primer 3 attaches a tail corresponding to the 3′ end of the IRESsequence to the α-lactalbumin signal peptide coding region. As statedabove, the second triplet codon of the bovine α-lactalbumin signalpeptide was mutated to allow efficient translation from the IRESsequence. The resulting signal peptide PCR fragment contains NaeI, NcoI,EcoRV, XbaI, BglII and XhoI sites on the 3′ end.

After the IRES and signal peptide were amplified individually using theprimers shown above, the two reaction products were mixed and PCR wasperformed using primer 1 and primer 4. The resultant product of thisreaction is a spliced fragment that contains the IRES attached to thefull length α-lactalbumin signal peptide. The ATG encoding the start ofthe signal peptide is placed at the same location as the ATG encodingthe start of the neomycin phosphotransferase gene found in the vectorpLXIN. The fragment also contains the EcoRI site on the 5′ end and NaeI,NcoI, EcoRV, XbaI, BglII and XhoI sites on the 3′ end.

The spliced IRES/α-lactalbumin signal peptide PCR fragment was digestedwith EcoRI and XhoI. The α-LA Signal Peptide vector construct was alsodigested with EcoRI and XhoI. These two fragments were ligated togetherto give the pIRES construct.

The IRES/α-lactalbumin signal peptide portion of the pIRES vector wassequenced and found to contain mutations in the 5′ end of the IRES.These mutations occur in a long stretch of C's and were found in allclones that were isolated.

To repair this problem, pLXIN DNA was digested with EcoRI and BsmFI. The500 bp band corresponding to a portion of the IRES sequence wasisolated. The mutated IRES/α-lactalbumin signal peptide construct wasalso digested with EcoRI and BsmFI and the mutated IRES fragment wasremoved. The IRES fragment from pLXIN was then substituted for the IRESfragment of the mutated IRES/α-lactalbumin signal peptide construct. TheIRES/α-LA signal peptide portion of resulting plasmid was then verifiedby DNA sequencing.

The resulting construct was found to have a number of sequencedifferences when compared to the expected pLXIN sequence obtained fromClontech. We also sequenced the IRES portion of pLXIN purchased fromClontech to verify its sequence. The differences from the expectedsequence also appear to be present in the pLXIN plasmid that we obtainedfrom Clontech. Four sequence differences were identified:

-   -   bp 347 T—was G in pLXIN sequence    -   bp 786-788 ACG—was GC in LXIN sequence.

B. CMV LL2

The CMV LL2 (SEQ ID NO:5; LL2 antibody is described in U.S. Pat. No.6,187,287, incorporated herein by reference) construct comprises thefollowing elements, arranged in 5′ to 3′ order: 5′CMV promoter(Clonetech), LL2 heavy chain signal peptide, LL2 antibody heavy chain;IRES from encephalomyocarditis virus; bovine α-LA signal peptide; LL2antibody light chain; and 3′ MoMuLV LTR. In addition to sequencesdescribed in SEQ ID NO:5, the CMV LL2 vector further comprises a 5′MoMuLV LTR, a MoMuLV extended viral packaging signal, and a neomycinphosphotransferase gene (these additional elements are provided in SEQID NO:7).

This construct uses the 5′ MoMuLV LTR to control production of theneomycin phosphotransferase gene. The expression of LL2 antibody iscontrolled by the CMV promoter (Clontech). The LL2 heavy chain gene andlight chain gene are attached together by an IRES sequence. The CMVpromoter drives production of a mRNA containing the heavy chain gene andthe light chain gene attached by the IRES. Ribosomes attach to the mRNAat the CAP site and at the IRES sequence. This allows both heavy andlight chain protein to be produced from a single mRNA. The mRNAexpression from the LTR as well as from the CMV promoter is terminatedand poly adenylated in the 3′ LTR.

The IRES sequence (SEQ ID NO:3) comprises a fusion of the IRES from theplasmid pLXIN (Clontech) and the bovine alpha-lactalbumin signalpeptide. The initial ATG of the signal peptide was attached to the IRESto allow the most efficient translation initiation from the IRES. The 3′end of the signal peptide provides a multiple cloning site allowing easyattachment of any protein of interest to create a fusion protein withthe signal peptide. The IRES sequence can serve as a translationalenhancer as well as creating a second translation initiation site thatallows two proteins to be produced from a single mRNA.

The LL2 light chain gene was attached to the IRES α-lactalbumin signalpeptide as follows. The LL2 light chain was PCR amplified from thevector pCRLL2 using the following primers.

Primer 1 (SEQ ID NO: 16): 5′ CTACAGGTGTCCACGTCGACATCCAGCTGACCCAG 3′Primer 2 (SEQ ID NO: 17): 5′ CTGCAGAATAGATCTCTAACACTCTCCCCTGTTG 3′

These primers add a HincII site right at the start of the coding regionfor mature LL2 light chain. Digestion of the PCR product with HincIIgives a blunt end fragment starting with the initial GAC encoding matureLL2 on the 5′ end. Primer 2 adds a BglII site to the 3′ end of the generight after the stop codon. The resulting PCR product was digested withHincII and BglII and cloned directly into the IRES-Signal Peptideplasmid that was digested with Nael and BglII.

The Kozak sequence of the LL2 heavy chain gene was then modified. Thevector pCRMN14HC was digested with XhoI and AvrII to remove about a 400bp fragment. PCR was then used to amplify the same portion of the LL2heavy chain construct that was removed by the XhoI-AvrII digestion. Thisamplification also mutated the 5′ end of the gene to add a better Kozaksequence to the clone. The Kozak sequence was modified to resemble thetypical IgG Kozak sequence. The PCR primers are shown below.

Primer 1 (SEQ ID NO: 18):5′ CAGTGTGATCTCGAGAATTCAGGACCTCACCATGGGATGGAGCTGTA TCAT 3′ Primer 2 (SEQID NO: 19): 5′ AGGCTGTATTGGTGGATTCGTCT 3′

The PCR product was digested with XhoI and AvrII and inserted back intothe previously digested plasmid backbone.

The “good” Kozak sequence was then added to the light chain gene. The“good” Kozak LL2 heavy chain gene construct was digested with EcoRI andthe heavy chain gene containing fragment was isolated. The IRESα-Lactalbumin Signal Peptide LL2 light chain gene construct was alsodigested with EcoRI. The heavy chain gene was then cloned into the EcoRIsite of IRES light chain construct. This resulted in the heavy chaingene being placed at the 5′ end of the IRES sequence.

Next, a multiple cloning site was added into the LNCX retroviralbackbone plasmid. The LNCX plasmid was digested with HindIII and ClaI.Two oligonucleotide primers were produced and annealed together tocreate an double stranded DNA multiple cloning site. The followingprimers were annealed together.

Primer 1 (SEQ ID NO: 20): 5′ AGCTTCTCGAGTTAACAGATCTAGGCCTCCTAGGTCGACAT3′ Primer 2 (SEQ ID NO: 21): 5′ CGATGTCGACCTAGGAGGCCTAGATCTGTTAACTCGAGA3′

After annealing, the multiple cloning site was ligated into LNCX tocreate LNC-MCS.

Next, the double chain gene fragment was ligated into the retroviralbackbone gene construct. The double chain gene construct created abovewas digested with SalI and BglII and the double chain containingfragment was isolated. The retroviral expression plasmid LNC-MCS wasdigested with XhoI and BglII. The double chain fragment was then clonedinto the LNC-MCS retroviral expression backbone.

Next, an RNA splicing problem in the construct was corrected. Theconstruct was digested with NsiI. The resulting fragment was thenpartially digested with EcoRI. The fragments resulting from the partialdigest that were approximately 9300 base pairs in size were gelpurified. A linker was created to mutate the splice donor site at the 3′end of the LL2 heavy chain gene. The linker was again created byannealing two oligonucleotide primers together to form the doublestranded DNA linker. The two primers used to create the linker are shownbelow.

Primer 1 (SEQ ID NO: 22):5′ CGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTC CCGGGAAATGAAAGCCG 3′Primer 2 (SEQ ID NO: 23):5′ AATTCGGCTTTCATTTCCCGGGAGACAGGGAGAGGCTCTTCTGCGTGTAGTGGTTGTGCAGAGCCTCGTGCA 3′

After annealing the linker was substituted for the original NsiI/EcoRIfragment that was removed during the partial digestion.

C. MMTV MN14

The MMTV MN14 (SEQ ID NO:6) construct comprises the following elements,arranged in 5′ to 3′ order: 5′ MMTV promoter; double mutated PPEsequence; MN14 antibody heavy chain; IRES from encephalomyocarditisvirus; bovine αLA signal peptide MN 14 antibody light chain; WPREsequence; and 3′ MoMuLV LTR. In addition to the sequences described inSEQ ID NO:6, the MMTV MN14 vector further comprises a MoMuLV LTR, MoMuLVextended viral packaging signal; neomycin phosphotransferase genelocated 5′ of the MMTV promoter (these additional elements are providedin SEQ ID NO: 7).

This construct uses the 5′ MoMuLV LTR to control production of theneomycin phosphotransferase gene. The expression of MN14 antibody iscontrolled by the MMTV promoter (Pharmacia). The MN14 heavy chain geneand light chain gene are attached together by an IRES/bovine α-LA signalpeptide sequence (SEQ ID NO: 3). The MMTV promoter drives production ofa mRNA containing the heavy chain gene and the light chain gene attachedby the IRES/bovine α-LA signal peptide sequence. Ribosomes attach to themRNA at the CAP site and at the IRES/bovine α-LA signal peptidesequence. This allows both heavy and light chain protein to be producedfrom a single mRNA. In addition, there are two genetic elementscontained within the mRNA to aid in export of the mRNA from the nucleusto the cytoplasm and aid in poly-adenylation of the mRNA. The PPEsequence is contained between the RNA CAP site and the start of the MN14protein coding region, the WPRE is contained between the end of MN14protein coding and the poly-adenylation site. The mRNA expression fromthe LTR as well as from the MMTV promoter is terminated andpoly-adenylated in the 3′ LTR.

ATG sequences within the PPE element (SEQ ID NO:2) were mutated toprevent potential unwanted translation initiation. Two copies of thismutated sequence were used in a head to tail array. This sequence isplaced just downstream of the promoter and upstream of the Kozaksequence and signal peptide-coding region. The WPRE is isolated fromwoodchuck hepatitis virus and also aids in the export of mRNA from thenucleus and creating stability in the mRNA. If this sequence is includedin the 3′ untranslated region of the RNA, level of protein expressionfrom this RNA increases up to 10-fold.

D. α-LA MN14

The α-LA MN14 (SEQ ID NO:7) construct comprises the following elements,arranged in 5′ to 3′ order: 5′ MoMuLV LTR, MoMuLV extended viralpackaging signal, neomycin phosphotransferase gene, bovine/humanalpha-lactalbumin hybrid promoter, double mutated PPE element, MN14heavy chain signal peptide, MN14 antibody heavy chain, IRES fromencephalomyocarditis virus/bovine αLA signal peptide, M14 antibody lightchain, WPRE sequence; and 3′ MoMuLV LTR.

This construct uses the 5′ MoMuLV LTR to control production of theneomycin phosphotransferase gene. The expression of MN14 antibody iscontrolled by the hybrid α-LA promoter (SEQ ID NO:1). The MN14 heavychain gene and light chain gene are attached together by an IRESsequence/bovine α-LA signal peptide (SEQ ID NO:3). The α-LA promoterdrives production of a mRNA containing the heavy chain gene and thelight chain gene attached by the IRES. Ribosomes attach to the mRNA atthe CAP site and at the IRES sequence. This allows both heavy and lightchain protein to be produced from a single mRNA.

In addition, there are two genetic elements contained within the mRNA toaid in export of the mRNA from the nucleus to the cytoplasm and aid inpoly-adenylation of the mRNA. The mutated PPE sequence (SEQ ID NO:2) iscontained between the RNA CAP site and the start of the MN14 proteincoding region. ATG sequences within the PPE element (SEQ ID NO:2) weremutated to prevent potential unwanted translation initiation. Two copiesof this mutated sequence were used in a head to tail array. Thissequence is placed just downstream of the promoter and upstream of theKozak sequence and signal peptide-coding region. The WPRE was isolatedfrom woodchuck hepatitis virus and also aids in the export of mRNA fromthe nucleus and creating stability in the mRNA. If this sequence isincluded in the 3′ untranslated region of the RNA, level of proteinexpression from this RNA increases up to 10-fold. The WPRE is containedbetween the end of MN14 protein coding and the poly-adenylation site.The mRNA expression from the LTR as well as from the bovine/humanalpha-lactalbumin hybrid promoter is terminated and poly adenylated inthe 3′ LTR.

The bovine/human alpha-lactalbumin hybrid promoter (SEQ ID NO:1) is amodular promoter/enhancer element derived from human and bovinealpha-lactalbumin promoter sequences. The human portion of the promoteris from +15 relative to transcription start point (tsp) to −600 relativeto the tsp. The bovine portion is then attached to the end of the humanportion and corresponds to −550 to −2000 relative to the tsp. The hybridwas developed to remove poly-adenylation signals that were present inthe bovine promoter and hinder retroviral RNA production. It was alsodeveloped to contain genetic control elements that are present in thehuman gene, but not the bovine.

For construction of the bovine/human α-lactalbumin promoter, humangenomic DNA was isolated and purified. A portion of the humanα-lactalbumin promoter was PCR amplified using the following twoprimers:

Primer 1 (SEQ ID NO: 24): 5′ AAAGCATATGTTCTGGGCCTTGTTACATGGCTGGATTGGTT3′ Primer 2 (SEQ ID NO: 25):5′ TGAATTCGGCGCCCCCAAGAACCTGAAATGGAAGCATCACTCAGTTT CATATAT 3′

This two primers created a NdeI site on the 5′ end of the PCR fragmentand a EcoRI site on the 3′ end of the PCR fragment.

The human PCR fragment created using the above primers was doubledigested with the restriction enzymes NdeI and EcoRI. The plasmidpKBaP-1 was also double digested with NdeI and EcoRI. The plasmidpKBaP-1 contains the bovine α-lactalbumin 5′ flanking region attached toa multiple cloning site. This plasmid allows attachment of various genesto the bovine α-lactalbumin promoter.

Subsequently, the human fragment was ligated/substituted for the bovinefragment of the promoter that was removed from the pKBaP-1 plasmidduring the double digestion. The resulting plasmid was confirmed by DNAsequencing to be a hybrid of the Bovine and Human a-lactalbuminpromoter/regulatory regions.

Attachment of the MN14 light chain gene to the IRES α-lactalbumin signalpeptide was accomplished as follows. The MN14 light chain was PCRamplified from the vector pCRMN14LC using the following primers.

Primer 1 (SEQ ID NO: 26): 5′ CTACAGGTGTCCACGTCGACATCCAGCTGACCCAG 3′Primer 2 (SEQ ID NO: 27): 5′ CTGCAGAATAGATCTCTAACACTCTCCCCTGTTG 3′

These primers add a HincII site right at the start of the coding regionfor mature MN14 light chain. Digestion of the PCR product with HincIIgives a blunt end fragment starting with the initial GAC encoding matureMN14 on the 5′ end. Primer 2 adds a BglII site to the 3′ end of the generight after the stop codon. The resulting PCR product was digested withHincII and BglII and cloned directly into the IRES-Signal Peptideplasmid that was digested with NaeI and BglII.

Next, the vector pCRMN14HC was digested with XhoI and NruI to removeabout a 500 bp fragment. PCR was then used to amplify the same portionof the MN14 heavy chain construct that was removed by the XhoI-NruIdigestion. This amplification also mutated the 5′ end of the gene to adda better Kozak sequence to the clone. The Kozak sequence was modified toresemble the typical IgG Kozak sequence. The PCR primers are shownbelow.

Primer 1 (SEQ ID NO: 28):5′ CAGTGTGATCTCGAGAATTCAGGACCTCACCATGGGATGGAGCTGTA TCAT 3′ Primer 2 (SEQID NO: 29): 5′ GTGTCTTCGGGTCTCAGGCTGT 3′

The PCR product was digested with XhoI and NruI and inserted back intothe previously digested plasmid backbone.

Next, the “good” Kozak MN14 heavy chain gene construct was digested withEcoRI and the heavy chain gene containing fragment was isolated. TheIRES α-Lactalbumin Signal Peptide MN14 light chain gene construct wasalso digested with EcoRI. The heavy chain gene was then cloned into theEcoRI site of IRES light chain construct. This resulted in the heavychain gene being placed at the 5′ end of the IRES sequence.

A multiple cloning site was then added to the LNCX retroviral backboneplasmid. The LNCX plasmid was digested with HindIII and ClaI. Twooligonucleotide primers were produced and annealed together to create andouble stranded DNA multiple cloning site. The following primers wereannealed together.

Primer 1 (SEQ ID NO: 30): 5′ AGCTTCTCGAGTTAACAGATCTAGGCCTCCTAGGTCGACAT3′ Primer 2 (SEQ ID NO: 31): 5′ CGATGTCGACCTAGGAGGCCTAGATCTGTTAACTCGAGA3′After annealing the multiple cloning site was ligated into LNCX tocreate LNC-MCS.

The double chain gene fragment was then inserted into a retroviralbackbone gene construct. The double chain gene construct created in step3 was digested with SalI and BglII and the double chain containingfragment was isolated. The retroviral expression plasmid LNC-MCS wasdigested with XhoI and BglII. The double chain fragment was then clonedinto the LNC-MCS retroviral expression backbone.

Next, a RNA splicing problem in the construct was repaired. Theconstruct was digested with NsiI. The resulting fragment was thenpartially digested with EcoRI. The fragments resulting from the partialdigest that were approximately 9300 base pairs in size, were gelpurified. A linker was created to mutate the splice donor site at the 3′end of the MN14 heavy chain gene. The linker was again created byannealing two oligonucleotide primers together to form the doublestranded DNA linker. The two primers used to create the linker are shownbelow.

Primer 1 (SEQ ID NO: 32):5′ CGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTC CCGGGAAATGAAAGCCG 3′Primer 2 (SEQ ID NO: 33):5′ AATTCGGCTTTCATTTCCCGGGAGACAGGGAGAGGCTCTTCTGCGTGTAGTGGTTGTGCAGAGCCTCGTGCA 3′

After annealing the linker was substituted for the original NsiI/EcoRIfragment that was removed during the partial digestion.

Next, the mutated double chain fragment was inserted into theα-Lactalbumin expression retroviral backbone LN α-LA-Mertz-MCS. The geneconstruct produced above was digested with BamHI and BglII and themutated double chain gene containing fragment was isolated. The LNα-LA-Mertz-MCS retroviral backbone plasmid was digested with BglII. TheBamHI/BglII fragment was then inserted into the retroviral backboneplasmid.

A WPRE element was then inserted into the gene construct. The plasmidBluescriptII SK+ WPRE-B11 was digested with BamHI and HincII to removethe WPRE element and the element was isolated. The vector created abovewas digested with BglII and HpaI. The WPRE fragment was ligated into theBglII and HpaI sites to create the final gene construct.

E. α-LA Bot

The α-LA Bot (SEQ ID NO:8, botulinum toxin antibody) construct comprisesthe following elements, arranged in 5′ to 3′ order: bovine/humanalpha-lactalbumin hybrid promoter, mutated PPE element, cc49 signalpeptide, botulinum toxin antibody light chain, IRES fromencephalomyocarditis virus/bovine α-LA signal peptide, botulinum toxinantibody heavy chain, WPRE sequence, and 3′ MoMuLV LTR. In addition, theα-LA botulinum toxin antibody vector further comprises a 5′ MoMuLV LTR,a MoMuLV extended viral packaging signal, and a neomycinphosphotransferase gene (these additional elements are provided in SEQID NO: 7).

This construct uses the 5′ MoMuLV LTR to control production of theneomycin phosphotransferase gene. The expression of botulinum toxinantibody is controlled by the hybrid a-LA promoter. The botulinum toxinantibody light chain gene and heavy chain gene are attached together byan IRES/bovine α-LA signal peptide sequence. The bovine/humanalpha-lactalbumin hybrid promoter drives production of a mRNA containingthe light chain gene and the heavy chain gene attached by the IRES.Ribosomes attach to the mRNA at the CAP site and at the IRES sequence.This allows both light and heavy chain protein to be produced from asingle mRNA.

In addition, there are two genetic elements contained within the mRNA toaid in export of the mRNA from the nucleus to the cytoplasm and aid inpoly-adenylation of the mRNA. The mutated PPE sequence (SEQ ID NO:2) iscontained between the RNA CAP site and the start of the MN14 proteincoding region. ATG sequences within the PPE element (SEQ ID NO:2) weremutated to prevent potential unwanted translation initiation. Two copiesof this mutated sequence were used in a head to tail array. Thissequence was placed just downstream of the promoter and upstream of theKozak sequence and signal peptide-coding region. The WPRE was isolatedfrom woodchuck hepatitis virus and also aids in the export of mRNA fromthe nucleus and creating stability in the mRNA. If this sequence isincluded in the 3′ untranslated region of the RNA, level of proteinexpression from this RNA increases up to 10-fold. The WPRE is containedbetween the end of MN14 protein coding and the poly-adenylation site.The mRNA expression from the LTR as well as from the bovine/humanalpha-lactalbumin hybrid promoter is terminated and poly adenylated inthe 3′ LTR.

The bovine/human α-lactalbumin hybrid promoter (SEQ ID NO:1) is amodular promoter/enhancer element derived from human and bovineα-lactalbumin promoter sequences. The human portion of the promoter isfrom +15 relative to transcription start point to −600 relative to thetsp. The bovine portion is then attached to the end of the human portionand corresponds to −550 to −2000 relative to the tsp. The hybrid wasdeveloped to remove poly-adenylation signals that were present in thebovine promoter and hinder retroviral RNA production. It was alsodeveloped to contain genetic control elements that are present in thehuman gene, but not the bovine. Likewise, the construct contains controlelements present in the bovine but not in the human.

F. LSRNL

The LSRNL (SEQ ID NO:9) construct comprises the following elements,arranged in 5′ to 3′ order: 5′ MoMuLV LTR, MoMuLV viral packagingsignal; hepatitis B surface antigen; RSV promoter; neomycinphosphotransferase gene; and 3′ MoMuLV LTR.

This construct uses the 5′ MoMuLV LTR to control production of theHepatitis B surface antigen gene. The expression of the neomycinphosphotransferase gene is controlled by the RSV promoter. The mRNAexpression from the LTR as well as from the RSV promoter is terminatedand poly adenylated in the 3′ LTR.

G. α-LA cc49IL2

The α-LA cc49IL2 (SEQ ID NO:10; the cc49 antibody is described in U.S.Pat. Nos. 5,512,443; 5,993,813; and 5,892,019; each of which is hereinincorporated by reference) construct comprises the following elements,arranged in 5′ to 3′ order: 5′ bovine/human α-lactalbumin hybridpromoter; cc49-IL2 coding region; and 3′ MoMuLV LTR. This gene constructexpresses a fusion protein of the single chain antibody cc49 attached toInterleukin-2. Expression of the fusion protein is controlled by thebovine/human α-lactalbumin hybrid promoter.

The bovine/human α-lactalbumin hybrid promoter (SEQ ID NO:1) is amodular promoter/enhancer element derived from human and bovinealpha-lactalbumin promoter sequences. The human portion of the promoteris from +15 relative to transcription start point to −600 relative tothe tsp. The bovine portion is then attached to the end of the humanportion and corresponds to −550 to −2000 relative to the tsp. The hybridwas developed to remove poly-adenylation signals that were present inthe bovine promoter and hinder retroviral RNA production. It was alsodeveloped to contain genetic control elements that are present in thehuman gene, but not the bovine. Likewise, the construct contains controlelements present in the bovine but not in the human. The 3′ viral LTRprovide the poly-adenylation sequence for the mRNA.

H. α-LA YP

The α-LA YP (SEQ ID NO: 11) construct comprises the following elements,arranged in 5′ to 3′ order: 5′ bovine/human alpha-lactalbumin hybridpromoter; double mutated PPE sequence; bovine αLA signal peptide;Yersenia pestis antibody heavy chain Fab coding region; EMCV IRES/bovineα-LA signal peptide; Yersenia pestis antibody light chain Fab codingregion; WPRE sequence; 3′ MoMuLV LTR.

This gene construct will cause the expression of Yersenia pestis mouseFab antibody. The expression of the gene construct is controlled by thebovine/human α-lactalbumin hybrid promoter. The PPE sequence and theWPRE sequence aid in moving the mRNA from the nucleus to the cytoplasm.The IRES sequence allows both the heavy and the light chain genes to betranslated from the same mRNA. The 3′ viral LTR provides thepoly-adenylation sequence for the mRNA.

In addition, there are two genetic elements contained within the mRNA toaid in export of the mRNA from the nucleus to the cytoplasm and aid inpoly-adenylation of the mRNA. The mutated PPE sequence (SEQ ID NO:2) iscontained between the RNA CAP site and the start of the MN14 proteincoding region. ATG sequences within the PPE element (SEQ ID NO:2) weremutated (bases 4, 112, 131, and 238 of SEQ ID NO: 2 were changed from aG to a T) to prevent potential unwanted translation initiation. Twocopies of this mutated sequence were used in a head to tail array. Thissequence was placed just downstream of the promoter and upstream of theKozak sequence and signal peptide-coding region. The WPRE was isolatedfrom woodchuck hepatitis virus and also aids in the export of mRNA fromthe nucleus and creating stability in the mRNA. If this sequence isincluded in the 3′ untranslated region of the RNA, level of proteinexpression from this RNA increases up to 10-fold. The WPRE is containedbetween the end of MN14 protein coding and the poly-adenylation site.The mRNA expression from the LTR as well as from the bovine/humanalpha-lactalbumin hybrid promoter is terminated and poly adenylated inthe 3′ LTR.

The bovine/human alpha-lactalbumin hybrid promoter (SEQ ID NO:1) is amodular promoter/enhancer element derived from human and bovinealpha-lactalbumin promoter sequences. The human portion of the promoteris from +15 relative to transcription start point to −600 relative tothe tsp. The bovine portion is then attached to the end of the humanportion and corresponds to −550 to −2000 relative to the tsp. The hybridwas developed to remove poly-adenylation signals that were present inthe bovine promoter and hinder retroviral RNA production. It was alsodeveloped to contain genetic control elements that are present in thehuman gene, but not the bovine. Likewise, the construct contains controlelements present in the bovine but not in the human.

EXAMPLE 2 Generation of Cell Lines Stably Expressing the MoMLV gag andpol Proteins

Examples 2-5 describe the production of pseudotyped retroviral vectors.These methods are generally applicable to the production of the vectorsdescribed above. The expression of the fusogenic VSV G protein on thesurface of cells results in syncytium formation and cell death.Therefore, in order to produce retroviral particles containing the VSV Gprotein as the membrane-associated protein a two-step approach wastaken. First, stable cell lines expressing the gag and pol proteins fromMoMLV at high levels were generated (e.g., 293GP^(SD) cells). The stablecell line which expresses the gag and pol proteins producesnoninfectious viral particles lacking a membrane-associated protein(e.g., an envelope protein). The stable cell line was thenco-transfected, using the calcium phosphate precipitation, with VSV-Gand gene of interest plasmid DNAs. The pseudotyped vector generated wasused to infect 293GP^(SD) cells to produce stably transformed celllines. Stable cell lines can be transiently transfected with a plasmidcapable of directing the high level expression of the VSV G protein (seebelow). The transiently transfected cells produce VSV G-pseudotypedretroviral vectors which can be collected from the cells over a periodof 3 to 4 days before the producing cells die as a result of syncytiumformation.

The first step in the production of VSV G-pseudotyped retroviralvectors, the generation of stable cell lines expressing the MoMLV gagand pol proteins is described below. The human adenovirusAd-5-transformed embryonal kidney cell line 293 (ATCC CRL 1573) wascotransfected with the pCMVgag-pol and the gene encoding for phleomycin.pCMV gag-pol contains the MoMLV gag and pol genes under the control ofthe CMV promoter (pCMV gag-pol is available from the ATCC).

The plasmid DNA was introduced into the 293 cells using calciumphosphate co-precipitation (Graham and Van der Eb, Virol. 52:456[1973]). Approximately 5×10⁵ 293 cells were plated into a 100 mm tissueculture plate the day before the DNA co-precipitate was added. Stabletransformants were selected by growth in DMEM-high glucose mediumcontaining 10% FCS and 10 μg/ml phleomycin (selective medium). Colonieswhich grew in the selective medium were screened for extracellularreverse transcriptase activity (Goff et al., J. Virol. 38:239 [1981])and intracellular p30gag expression. The presence of p30gag expressionwas determined by Western blotting using a goat-anti p30 antibody (NClantiserum 77S000087). A clone which exhibited stable expression of theretroviral genes was selected. This clone was named 293GP^(SD) (293gag-pol-San Diego). The 293GP^(SD) cell line, a derivative of the humanAd-5-transformed embryonal kidney cell line 293, was grown in DMEM-highglucose medium containing 10% FCS.

EXAMPLE 3 Preparation of Pseudotyped Retroviral Vectors Bearing the GGlycoprotein of VSV

In order to produce VSV G protein pseudotyped retrovirus the followingsteps were taken. The 293GP^(SD) cell line was co-transfected with VSV-Gplasmid and DNA plasmid of interest. This co-transfection generates theinfectious particles used to infect 293GP^(SD) cells to generate thepackaging cell lines. This Example describes the production ofpseudotyped LNBOTDC virus. This general method may be used to produceany of the vectors described in Example 1.

a) Cell Lines and Plasmids

The packaging cell line, 293GP^(SD) was grown in alpha-MEM-high glucosemedium containing 10% FCS The titer of the pseudo-typed virus may bedetermined using either 208F cells (Quade, Virol. 98:461 [1979]) orNIH/3T3 cells (ATCC CRL 1658); 208F and NIH/3T3 cells are grown inDMEM-high glucose medium containing 10% CS.

The plasmid LNBOTDC contains the gene encoding BOTD under thetranscriptional control of cytomegalovirus intermediate-early promoterfollowed by the gene encoding neomycin phosphotransferase (Neo) underthe transcriptional control of the LTR promoter. The plasmid pHCMV-Gcontains the VSV G gene under the transcriptional control of the humancytomegalovirus intermediate-early promoter (Yee et al., Meth. CellBiol. 43:99 [1994]).

b) Production of Stable Packaging Cell Lines, Pseudotyped Vector andTitering of Pseudotyped LNBOTDC Vector

LNBOTDC DNA (SEQ ID NO: 13) was co-transfected with pHCMV-G DNA into thepackaging line 293GP^(SD) to produce LNBOTDC virus. The resultingLNBOTDC virus was then used to infect 293GP^(SD) cells to transform thecells. The procedure for producing pseudotyped LNBOTDC virus was carriedout as described (Yee et al., Meth. Cell Biol. 43:99 [1994].

This is a retroviral gene construct that upon creation of infectiousreplication defective retroviral vector will cause the insertion of thesequence described above into the cells of interest. Upon insertion theCMV regulatory sequences control the expression of the botulinum toxinantibody heavy and light chain genes. The IRES sequence allows both theheavy and the light chain genes to be translated from the same mRNA. The3′ viral LTR provides the poly-adenylation sequence for the mRNA.

Both heavy and light chain protein for botulinum toxin antibody areproduced from this signal mRNA. The two proteins associated to formactive botulinum toxin antibody. The heavy and light chain proteins alsoappear to be formed in an equal molar ratio to each other.

Briefly, on day 1, approximately 5×10⁴ 293GP^(SD) cells were placed in a75 cm² tissue culture flask. On the following day (day 2), the293GP^(SD) cells were transfected with 25 μg of pLNBOTDC plasmid DNA and25 μg of VSV-G plasmid DNA using the standard calcium phosphateco-precipitation procedure (Graham and Van der Eb, Virol. 52:456[1973]). A range of 10 to 40 μg of plasmid DNA may be used. Because293GP^(SD) cells may take more than 24 hours to attach firmly to tissueculture plates, the 293GP^(SD) cells may be placed in 75 cm2 flasks 48hours prior to transfection. The transfected 293GP^(SD) cells providepseudotyped LNBOTDC virus.

On day 3, approximately 1×10⁵ 293GP^(SD) cells were placed in a 75 cm²tissue culture flask 24 hours prior to the harvest of the pseudotypedvirus from the transfected 293GP^(SD) cells. On day 4, culture mediumwas harvested from the transfected 2093GP^(SD) cells 48 hours after theapplication of the pLNBOTDC and VSV-G DNA. The culture medium wasfiltered through a 0.45 μm filter and polybrene was added to a finalconcentration of 8 μg/ml. The culture medium containing LNBOTDC viruswas used to infect the 293GP^(SD) cells as follows. The culture mediumwas removed from the 293GP^(SD) cells and was replaced with the LNBOTDCvirus containing culture medium. Polybrene was added to the mediumfollowing addition to cells. The virus containing medium was allowed toremain on the 293GP^(SD) cells for 24 hours. Following the 16 hourinfection period (on day 5), the medium was removed from the 293GP^(SD)cells and was replaced with fresh medium containing 400 μg/ml G418(GIBCO/BRL). The medium was changed approximately every 3 days untilG418-resistant colonies appeared approximately two weeks later.

The G418-resistant 293 colonies were plated as single cells in 96 wells.Sixty to one hundred G418-resistant colonies were screened for theexpression of the BOTDC antibody in order to identify high producingclones. The top 10 clones in 96-well plates were transferred 6-wellplates and allowed to grow to confluency.

The top 10 clones were then expanded to screen for high titerproduction. Based on protein expression and titer production, 5 clonalcell lines were selected. One line was designated the master cell bankand the other 4 as backup cell lines. Pseudotyped vector was generatedas follows. Approximately 1×10⁶ 293GP^(SD)/LNBOTDC cells were placedinto a 75 cm² tissue culture flask. Twenty-four hours later, the cellswere transfected with 25 μg of pHCMV-G plasmid DNA using calciumphosphate co-precipitation. Six to eight hours after the calcium-DNAprecipitate was applied to the cells, the DNA solution was replaced withfresh culture medium (lacking G418). Longer transfection times(overnight) were found to result in the detachment of the majority ofthe 293GP^(SD)/LNBOTDC cells from the plate and are therefore avoided.The transfected 293GP^(SD)/LNBOTDC cells produce pseudotyped LNBOTDCvirus.

The pseudotyped LNBOTDC virus generated from the transfected293GP^(SD)/LNBOTDC cells can be collected at least once a day between 24and 96 hr after transfection. The highest virus titer was generatedapproximately 48 to 72 hr after initial pHCMV-G transfection. Whilesyncytium formation became visible about 48 hr after transfection in themajority of the transfected cells, the cells continued to generatepseudotyped virus for at least an additional 48 hr as long as the cellsremained attached to the tissue culture plate. The collected culturemedium containing the VSV G-pseudotyped LNBOTDC virus was pooled,filtered through a 0.45 μm filter and stored at −80° C. or concentratedimmediately and then stored at −80° C.

The titer of the VSV G-pseudotyped LNBOTDC virus was then determined asfollows. Approximately 5×10⁴ rat 208F fibroblasts cells were plated into6 well plates. Twenty-fours hours after plating, the cells were infectedwith serial dilutions of the LNBOTDC virus-containing culture medium inthe presence of 8 μg/ml polybrene. Twenty four hours after infectionwith virus, the medium was replaced with fresh medium containing 400μg/ml G418 and selection was continued for 14 days until G418-resistantcolonies became visible. Viral titers were typically about 0.5 to5.0×10⁶ colony forming units (cfu)/ml. The titer of the virus stockcould be concentrated to a titer of greater than 10⁹ cfu/ml as describedbelow.

EXAMPLE 4 Concentration of Pseudotyped Retroviral Vectors

The VSV G-pseudotyped LNBOTDC viruses were concentrated to a high titerby one cycle of ultracentrifugation. However, two cycles can beperformed for further concentration. The frozen culture medium collectedas described in Example 2 which contained pseudotyped LNBOTDC virus wasthawed in a 37° C. water bath and was then transferred to Oakridgecentrifuge tubes (50 ml Oakridge tubes with sealing caps, Nalge NuncInternational) previously sterilized by autoclaving. The virus wassedimented in a JA20 rotor (Beckman) at 48,000×g (20,000 rpm) at 4° C.for 120 min. The culture medium was then removed from the tubes in abiosafety hood and the media remaining in the tubes was aspirated toremove the supernatent. The virus pellet was resuspended to 0.5 to 1% ofthe original volume of culture medium DMEM. The resuspended virus pelletwas incubated overnight at 4° C. without swirling. The virus pelletcould be dispersed with gentle pipetting after the overnight incubationwithout significant loss of infectious virus. The titer of the virusstock was routinely increased 100- to 300-fold after one round ofultracentrifugation. The efficiency of recovery of infectious virusvaried between 30 and 100%.

The virus stock was then subjected to low speed centrifugation in amicrofuge for 5 min at 4° C. to remove any visible cell debris oraggregated virions that were not resuspended under the above conditions.It was noted that if the virus stock is not to be used for injectioninto oocytes or embryos, this centrifugation step may be omitted.

The virus stock can be subjected to another round of ultracentrifugationto further concentrate the virus stock. The resuspended virus from thefirst round of centrifugation is pooled and pelleted by a second roundof ultracentrifugation which is performed as described above. Viraltiters are increased approximately 2000-fold after the second round ofultracentrifugation (titers of the pseudotyped LNBOTDC virus aretypically greater than or equal to 1×10⁹ cfu/ml after the second roundof ultracentrifugation).

The titers of the pre- and post-centrifugation fluids were determined byinfection of 208F cells (NIH 3T3 or bovine mammary epithelial cells canalso be employed) followed by selection of G418-resistant colonies asdescribed above in Example 2.

EXAMPLE 5 Preparation of Pseudotyped Retrovirus for Infection of HostCells

The concentrated pseudotyped retroviruses were resuspended in 0.1×HBS(2.5 mM HEPES, pH 7.12, 14 mM NaCl, 75 μM Na₂HPO₄—H₂O) and 18 μlaliquots were placed in 0.5 ml vials (Eppendorf) and stored at −80° C.until used. The titer of the concentrated vector was determined bydiluting 1 μl of the concentrated virus 10⁻⁷- or 10⁻⁸-fold with 0.1×HBS.The diluted virus solution was then used to infect 208F and bovinemammary epithelial cells and viral titers were determined as describedin Example 2.

EXAMPLE 6 Expression of MN14 by Host Cells

This Example describes the production of antibody MN14 from cellstransfected with a high number of integrating vectors. Pseudotypedvector were made from the packaging cell lines for the followingvectors: CMV MN14, α-LA MN14, and MMTV MN14. Rat fibroblasts (208Fcells), MDBK cells (bovine kidney cells), and bovine mammary epithelialcells were transfected at a multiplicity of infection of 1000. Onethousand cells were plated in a T25 flask and 106 colony forming units(CFU's) of vector in 3 ml media was incubated with the cells. Theduration of the infection was 24 hr, followed by a media change.Following transfection, the cells were allowed to grow and becomeconfluent.

The cell lines were grown to confluency in T25 flasks and 5 ml of mediawas changed daily. The media was assayed daily for the presence of MN14.All of the MN14 produced is active (an ELISA to detect human IgG gavethe exact same values as the CEA binding ELISA) and Western blotting hasshown that the heavy and light chains are produced at a ratio thatappears to be a 1:1 ratio. In addition, a non-denaturing Western blotindicated that what appeared to be 100% of the antibody complexes werecorrectly formed (See FIG. 1: Lane 1, 85 ng control Mn14; Lane 2, bovinemammary cell line, α-LA promoter; Lane 3, bovine mammary cell line, CMVpromoter; Lane 4, bovine kidney cell line, α-LA promoter; Lane 5, bovinekidney cell line, CMV promoter; Lane 6, 208 cell line, α-LA promoter;Lane 7, 208 cell line, CMV promoter)).

FIG. 2 is a graph showing the production of MN14 over time for four celllines. The Y axis shows MN14 production in ng/ml of media. The X-axisshows the day of media collection for the experiment. Four sets of dataare shown on the graph. The comparisons are between the CMV and α-LApromoter and between the 208 cells and the bovine mammary cells. Thebovine mammary cell line exhibited the highest expression, followed bythe 208F cells and MDBK cells. With respect to the constructs, theCMV-driven construct demonstrated the highest level of expression,followed by the α-LA driven gene construct and the MMTV construct. At 2weeks, the level of daily production of the CMV construct was 4.5 μg/mlof media (22.5 mg/day in a T25 flask). The level of expressionsubsequently increased slowly to 40 μg/day as the cells became verydensely confluent over the subsequent week. 2.7 L of media from anα-lac-MN14 packaging cell line was processed by affinity chromatographyto produce a purified stock of MN14.

FIG. 3 is a western blot of a 15% SDS-PAGE gel run under denaturingconditions in order to separate the heavy and light chains of the MN14antibody. Lane 1 shows MN14 from bovine mammary cell line, hybrid α-LApromoter; lane 2 shows MN14 from bovine mammary cell line, CMV promoter;lane 3 shows MN14 from bovine kidney cell line, hybrid αLA promoter;lane 4 shows MN14 from bovine kidney cell line, CMV promoter; lane 5shows MN14 from rat fibroblast cell line, hybrid α-LA promoter; lane 6shows MN14 from rat fibroblast, CMV promoter. In agreement with FIG. 1above, the results show that the heavy and light chains are produced ina ratio of approximately 1:1.

EXAMPLE 7 Quantitation of Protein Produced Per Cell

This Example describes the quantitation of the amount of proteinproduced per cell in cell cultures produced according to the invention.Various cells (208F cells, MDBK cells, and bovine mammary cells) wereplated in 25 cm² culture dishes at 1000 cells/dish. Three differentvectors were used to infect the three cells types (CMV-MN14, MMTV-MN14,and α-LA-MN14) at an MOI of 1000 (titers: 2.8×10⁶, 4.9×10⁶, and 4.3×10⁶,respectively). Media was collected approximately every 24 hours from allcells. Following one month of media collection, the 208F and MDBK cellswere discarded due to poor health and low MN14 expression. The cellswere passaged to T25 flasks and collection of media from the bovinemammary cells was continued for approximately 2 months with continuedexpression of MN14. After two months in T25 flasks, the cells with CMVpromoters were producing 22.5 pg/cell/day and the cells with α-LApromoters were producing 2.5 pg MN14/cell/day.

After 2 months in T25 flasks, roller bottles (850 cm²) were seeded toscale-up production and to determine if MN14 expression was stablefollowing multiple passages. Two roller bottles were seeded with bovinemammary cells expressing MN14 from a CMV promoter and two roller bottleswere seeded with bovine mammary cells expressing MN14 from the α-LApromoter. The cultures reached confluency after approximately two weeksand continue to express MN14. Roller bottle expression is shown in Table1 below.

TABLE 1 Production of MN14 in Roller Bottles MN14 MN14 Production/Production/ Week - Total Cell Line Promoter Week (μg/ml) (μg/ml) BovineCMV 2.6 1 - 520 mammary Bovine CMV 10.6 2 - 2120 mammary Bovine CMV 8.73 - 1740 mammary Bovine CMV 7.8 4 - 1560 mammary Bovine α-LA 0.272 1 -54.4 mammary Bovine α-LA 2.8 2 - 560 mammary Bovine α-LA 2.2 3 - 440mammary Bovine α-LA 2.3 4 - 460 mammary

EXAMPLE 8 Transfection at Varied Multiplicities of Infection

This Example describes the effect of transfection at variedmultiplicities of infection on protein expression. 208F rat fibroblastand bovine mammary epithelial cells (BMEC) were plated in a 25 cm²plates at varied cell numbers/25 cm². Cells were infected with eitherthe CMV MN14 vector or the αLA MN14 vector at a MOI of 1,10, 1000, and10,000 by keeping the number of CFUs kept constant and varying thenumber of cells infected.

Following infection, medium was changed daily and collectedapproximately every 24 hours from all cells for approximately 2 months.The results of both of the vectors in bovine mammary epithelial cellsare shown in Table 2 below. Cells without data indicate cultures thatbecame infected prior to the completion of the experiment. The “# cells”column represents the number of cells at the conclusion of theexperiment. The results indicate that a higher MOI results in increasedMN14 production, both in terms of the amount of protein produced perday, and the total accumulation.

TABLE 2 MOI vs. Protein Production MN14 % cell Production/ Cell Con-MN14 day Line Promoter MOI fluency (ng/ml) # Cells (pg/cell) BMEC CMV10000 100% 4228 4.5E5 47 BMEC CMV 1000 100% 2832 2.0E6 7.1 BMEC CMV 100BMEC CMV 10 100% 1873 2.5E6 3.75 BMEC CMV 1 BMEC αLA 10000 100% 10241.5E6 3.4 BMEC αLA 1000 BMEC αLA 100 100% 722 1.8E6 1.9 BMEC αLA 10 100%421234 2.3E6 .925 BMEC αLA 1 100% 1.9E6 .325

EXAMPLE 9 Transfection at Varied Multiplicities of Infection

This experiment describes protein production from the CMV MN14 vector ata variety of MOI values. Bovine mammary cells, CHO cells, and humanembryo kidney cells (293 cells) were plated in 24 well plates (2 cm²) at100 cells/2 cm² well. Cells were infected at various dilutions with CMVMN14 to obtain MOI values of 1, 10, 100, 1000, and 10000. The CHO cellsreached confluency at all MOI within 11 days of infection. However, thecells infected at a MOI of 10,000 grew more slowly. The bovine mammaryand 293 cells grew slower, especially at the highest MOI of 10,000. Thecells were then passaged into T25 flasks to disperse cells. Followingdispersion, cells reached confluence within 1 week. the medium wascollected after one week and analyzed for MN14 production. The CHO andhuman 293 cells did not exhibit good growth in extended culture. Thus,data were not collected from these cells. Data for bovine mammaryepithelial cells are shown in Table 3 below. The results indicate thatproduction of MN14 increased with higher MOI.

TABLE 3 MOI vs. Protein Production MN14 Production Cell Line PromoterMOI % confluency (ng/ml) BMEC CMV 10000 100% 1312 BMEC CMV 1000 100% 100BMEC CMV 100 100% 7.23 BMEC CMV 10 100% 0 BMEC CMV 1 100% 0

EXAMPLE 10 Expression of LL2 Antibody by Bovine Mammary Cells

This Example describes the expression of antibody LL2 by bovine mammarycells. Bovine mammary cells were infected with vector CMV LL2 (7.85×10⁷CFU/ml) at MOI's of 1000 and 10,000 and plated in 25 cm² culture dishes.None of the cells survived transfection at the MOI of 10,000. At 20%confluency, 250 ng/ml of LL2 was present in the media.

EXAMPLE 11 Expression of Botulinum Toxin Antibody by Bovine MammaryCells

This Example describes the expression of Botulinum toxin antibody inbovine mammary cells. Bovine mammary cells were infected with vectorα-LA Bot (2.2×10² CFU/ml) and plated in 25 cm² culture dishes. At 100%confluency, 6 ng/ml of Botulinum toxin antibody was present in themedia.

EXAMPLE 12 Expression of Hepatitis B Surface Antigen by Bovine MammaryCells

This Example describes the expression of hepatitis B surface antigen(HBSAg) in bovine mammary cells. Bovine mammary cells were infected withvector LSRNL (350 CFU/ml) and plated in 25 cm² culture dishes. At 100%confluency, 20 ng/ml of HBSAg was present in the media.

EXAMPLE 13 Expression of cc49IL2 Antigen Binding Protein by BovineMammary Cells

This Example describes the expression of cc49IL2 in bovine mammarycells. Bovine mammary cells were infected with vector cc49IL2 (3.1×10⁵CFU/ml) at a MOI of 1000 and plated in 25 cm² culture dishes. At 100%confluency, 10 μg/ml of cc49IL2 was present in the media.

EXAMPLE 14 Expression of Multiple Proteins by Bovine Mammary Cells

This Example describes the expression of multiple proteins in bovinemammary cells. Mammary cells producing MN14 (infected with CMV-MN14vector) were infected with cc49IL2 vector (3.1×10⁵ CFU/ml) at an MOI of1000, and 1000 cells were plated in 25 cm² culture plates. At 100%confluency, the cells expressed MN14 at 2.5 μg/ml and cc49IL2 at 5μg/ml.

EXAMPLE 15 Expression of Multiple Proteins by Bovine Mammary Cells

This Example describes the expression of multiple proteins in bovinemammary cells. Mammary cells producing MN14 (infected with CMV-MN14vector) were infected with LSNRL vector (100 CFU/ml) at an MOI of 1000,and 1000 cells were plated in 25 cm² culture plates. At 100% confluency,the cells expressed MN14 at 2.5 μg/ml and hepatitis surface antigen at150 ng/ml.

EXAMPLE 16 Expression of Multiple Proteins by Bovine Mammary Cells

This Example describes the expression of multiple proteins in bovinemammary cells. Mammary cells producing hepatitis B surface antigen(infected with LSRNL vector) were infected with cc49IL2 vector at an MOIof 1000, and 1000 cells were plated in 25 cm² culture plates. At 100%confluency, the cells expressed MN14 at 2.4 μg/ml and hepatitis Bsurface antigen at 13 ng/ml. It will be understood that multipleproteins may be expressed in the other cell lines described above.

EXAMPLE 17 Expression of Hepatitis B Surface Antigen and Botulinum ToxinAntibody in Bovine Mammary Cells

This Example describes the culture of transfected cells in roller bottlecultures. 208F cells and bovine mammary cells were plated in 25 cm²culture dishes at 1000 cells/25 cm². LSRNL or α-LA Bot vectors were usedto infect each cell line at a MOI of 1000. Following one month ofculture and media collection, the 208F cells were discarded due to poorgrowth and plating. Likewise, the bovine mammary cells infected withα-LA Bot were discarded due to low protein expression. The bovinemammary cells infected with LSRNL were passaged to seed roller bottles(850 cm²). Approximately 20 ng/ml hepatitis type B surface antigen wasproduced in the roller bottle cultures.

EXAMPLE 18 Expression in Clonally Selected Cell Lines

This experiment describes expression of MN14 from clonally selected celllines. Cell lines were grown to confluency in T25 flasks and 5 ml ofmedia were collected daily. The media was assayed daily for the presenceof MN14. All the MN14 produced was active and Western blotting indicatedthat the heavy and light chains were produce at a ratio that appears tobe almost exactly 1:1. In addition, a non-denaturing western blotindicated that approximately 100% of the antibody complexes werecorrectly formed. After being in culture for about two months, the cellswere expanded into roller bottles or plated as single cell clones in 96well plates.

The production of MN14 in the roller bottles was analyzed for a 24 hourperiod to determine if additional medium changing would increaseproduction over what was obtained with weekly medium changes. Three 24hour periods were examined. The CMV promoter cells in 850 cm² rollerbottles produced 909 ng/ml the first day, 1160 ng/ml the second day and1112 ng/ml the third day. The α-LA promoter cells produced 401 ng/ml thefirst day, 477 ng/ml the second day and 463 ng/ml the third day. Thesevalues correspond well to the 8-10 mg/ml/week that were obtained for theCMV cells and the 2-3 mg/ml that were obtained for the α-LA cells. Itdoes not appear that more frequent media changing would increase MN14production in roller bottles.

Single cell lines were established in 96 well plates and then passagedinto the same wells to allow the cells to grow to confluency. Once thecells reached confluency, they were assayed for MN14 production over a24 hour period. The clonal production of MN14 from CMV cell lines rangedfrom 19 ng/ml/day to 5500 ng/ml/day. The average production of all cellclones was 1984 ng/ml/day. The α-LA cell clones yielded similar results.The clonal production of MN14 from α-LA cell lines ranged from 1ng/ml/day to 2800 ng/ml/day. The average production of these cell cloneswas 622 ng/ml/day. The results are provided in Table 4 below.

TABLE 4 Expression in Clonal Cell Lines MN14 Alpha-lactalbumin CMVClonal Cell Production Clonal Cell Line MN14 Production Line Number(ng/ml) Number (ng/ml) 22 19 27 0 6 88 29 0 29 134 12 0.7 34 151 50 8 32221 28 55 23 343 43 57 27 423 8 81 4 536 13 154 41 682 48 159 45 685 7186 40 696 36 228 11 1042 39 239 8 1044 51 275 5 1066 31 283 19 1104 54311 48 1142 38 317 12 1224 21 318 26 1315 16 322 39 1418 47 322 37 161017 325 20 1830 37 367 21 1898 45 395 47 1918 25 431 35 1938 5 441 151968 20 449 3 1976 19 454 28 1976 22 503 1 2166 55 510 16 2172 14 519 172188 41 565 33 2238 46 566 30 2312 23 570 38 2429 1 602 2 2503 9 609 142564 53 610 24 2571 56 631 9 2708 2 641 42 2729 40 643 44 2971 32 653 73125 24 664 43 3125 26 671 25 3650 52 684 46 3706 6 693 50 3947 33 75849 4538 42 844 18 4695 10 1014 31 4919 3 1076 10 5518 44 1077 35 1469 341596 18 1820 30 2021 11 2585 4 2800

EXAMPLE 19 Estimation of Insert Copy Number

This example describes the relationship of multiplicity of infection,gene copy number, and protein expression. Three DNA assays weredeveloped using the INVADER Assay system (Third Wave Technologies,Madison, Wis.). One of the assays detects a portion of the bovineα-lactalbumin 5′ flanking region. This assay is specific for bovine anddoes not detect the porcine or human α-lactalbumin gene. This assay willdetect two copies of the α-lactalbumin gene in all control bovine DNAsamples and also in bovine mammary epithelial cells. The second assaydetects a portion of the extended packaging region from the MLV virus.This assay is specific for this region and does not detect a signal inthe 293 human cell line, bovine mammary epithelial cell line or bovineDNA samples. Theoretically, all cell lines or other samples not infectedwith MLV should not produce a signal. However, since the 293GP cell linewas produced with the extended packaging region of DNA, this cell linegives a signal when the assay is run. From the initial analysis, itappears that the 293GP cell line contains two copies of the extendedpacking region sequence that are detected by the assay. The final assayis the control assay. This assay detects a portion of the insulin-likegrowth factor I gene that is identical in bovine, porcine, humans and anumber of other species. It is used as a control on every sample that isrun in order to determine the amount of signal that is generated fromthis sample for a two copy gene. All samples that are tested shouldcontain two copies of the control gene.

DNA samples can be isolated using a number of methods. Two assays arethen performed on each sample. The control assay is performed along witheither the bovine α-lactalbumin assay or the extended packaging regionassay. The sample and the type of information needed will determinewhich assay is run. Both the control and the transgene detection assayare run on the same DNA sample, using the exact same quantity of DNA.

The data resulting from the assay are as follows (Counts indicatearbitrary fluorescence units):

-   -   Extended Packaging Region or α-Lactalbumin Background counts    -   Extended Packaging Region or α-Lactalbumin counts    -   Internal Control background counts    -   Internal Control counts

To determine net counts for the assay the background counts aresubtracted from the actual counts. This occurs for both the control andtransgene detection assay. Once the net counts are obtained, a ratio ofthe net counts for the transgene detection assay to the net counts ofthe control assay can be produced. This value is an indication of thenumber of copies of transgene compared to the number of copies of theinternal control gene (in this case IGF-I). Because the transgenedetection assay and the control assay are two totally different assays,they do not behave exactly the same. This means that one does not get anexact 1:1 ratio if there are two copies of the transgene and two copiesof the control gene in a specific sample. However the values aregenerally close to the 1:1 ratio. Also, different insertion sites forthe transgene may cause the transgene assay to behave differentlydepending on where the insertions are located.

Therefore, although the ratio is not an exact measure of copy number, itis a good indication of relative copy number between samples. Thegreater the value of the ratio the greater the copy number of thetransgene. Thus, a ranking of samples from lowest to highest will give avery accurate comparison of the samples to one another with regard tocopy number. Table 5 provides actual data for the EPR assay:

TABLE 5 Control Net Transgene Net Control Background Control TransgeneBackground Transgene Net Sample # Counts Counts Counts Counts CountsCounts Ratio 293  116 44 72 46.3 46 0.3 0 293GP 112 44 68 104 46 58 .841 74 40 34 88 41 47 1.38 2 64 40 24 83 41 43 1.75 3 62 44 18 144 46 985.57

From this data, it can be determined that the 293 cell line has nocopies of the extended packaging region/transgene. However the 293 GPcells appear to have two copies of the extended packaging region. Theother three cell lines appear to have three or more copies of theextended packaging region (one or more additional copies compared to293GP cells). Invader Assay Gene Ratio and Cell Line Protein ProductionBovine mammary epithelial cells were infected with either the CMV drivenMN14 construct or the α-lactalbumin driven MN14 construct. The cellswere infected at a 1000 to 1 vector to cell ratio. The infected cellswere expanded. Clonal cell lines were established for both the α-LA andCMV containing cells from this initial pooled population of cells.Approximately 50 cell lines were produced for each gene construct.Individual cells were placed in 96 well plates and then passaged intothe same well to allow the cells to grow to confluency. Once the cellslines reached confluency, they were assayed for MN14 production over a24 hour period. The clonal production of MN14 from CMV cell lines rangedfrom 0 ng/ml/day to 5500 ng/ml/day. The average production of all cellclones was 1984 ng/ml/day. The α-LA cell clones showed similar trends.The clonal production of MN14 from α-LA cell lines ranged from 0ng/ml/day to 2800 ng/ml/day. The average production of these cell cloneswas 622 ng/ml/day.

For further analysis of these clonal lines, fifteen CMV clones andfifteen α-LA clones were selected. Five highest expressing, five lowexpressing and five mid-level expressing lines were chosen. These thirtycell lines were expanded and banked. DNA was isolated from most all ofthe thirty cell lines. The cell lines were passed into 6 well plates andgrown to confluency. Once at confluency, the media was changed every 24hours and two separate collections from each cell line were assayed forMN14 production. The results of these two assays were averaged and thesenumbers were used to create Tables 6 and 7 below. DNA from the celllines was run using the Invader extended packaging region assay and theresults are shown below. The Tables show the cell line number,corresponding gene ratio and antibody production.

TABLE 6 CMV Clonal Cell Invader MN14 Production Line Number Gene Ratio(ng/ml)  6 0.19 104  7 1.62 2874 10 2.57 11202 18 3.12 7757 19 1.62 248321 1.53 3922 22 0 0 29 0.23 443 31 3.45 5697 32 0.27 346 34 0.37 305 381.47 2708 41 1.54 5434 49 2.6 7892 50 1.56 5022 Average of All 1.48 3746Clones

TABLE 7 α-LA Clonal Cell Invader MN14 Production Line Number Gene Ratio(ng/ml)  4 4.28 3600  6 1.15 959 12 0.35 21 17 0.54 538 28 0.75 60 301.73 2076 31 0.74 484 34 4.04 3332 41 1.33 771 Average of All 1.66 1316Clones

The graphs (FIGS. 17 and 18) show the comparison between proteinexpression and invader assay gene ratio. The results indicate that thereis a direct correlation between invader assay gene ratio and proteinproduction. It also appears that the protein production has not reacheda maximum and if cells containing a higher invader assay gene ratio wereproduced, higher protein production would occur.

Invader Assay Gene Ratio and Multiple Cell Line Infections

Two packaging cell lines (293GP) produced using previously describedmethods were used to produce replication defective retroviral vector.One of the cell lines contains a retroviral gene construct thatexpresses the botulinum toxin antibody gene from the CMV promoter(LTR-Extended Viral Packaging Region-Neo Gene-CMV Promoter-Bot LightChain Gene-IRES-Bot Heavy Chain Gene-LTR), the other cell line containsa retroviral gene construct that expresses the YP antibody gene from theCMV promoter (LTR-Extended Viral Packaging Region-Neo Gene-CMVPromoter-YP Heavy Chain Gene-IRES-YP Light Chain Gene-WPRE-LTR). Inaddition to being able to produce replication defective retroviralvector, each of these cell lines also produce either botulinum toxinantibody or YP antibody.

The vector produced from these cell lines was then used to re-infect theparent cell line. This procedure was performed in order to increase thenumber of gene insertions and to improve antibody production from thesecell lines. The botulinum toxin parent cell line was infected with a newaliquot of vector on three successive days. The titer of the vector usedto perform the infection was 1×10⁸ cfu/ml. Upon completion of the final24 hour infection, clonal selection was performed on the cells and thehighest protein producing line was established for botulinum toxinantibody production. A similar procedure was performed on the YP parentcell line. This cell line was also infected with a new aliquot of vectoron three successive days. The titer of the YP vector aliquots was 1×10⁴.Upon completion of the final 24 hour infection, clonal selection wasperformed on the cells and the highest protein producing line wasestablished for YP production.

Each of the parent cell lines and the daughter production cell lineswere examined for Invader gene ratio using the extended packaging regionassay and for protein production. The Bot production cell line which wasgenerated using the highest titer vector had the highest gene ratio. Italso had the highest protein production, again suggesting that gene copynumber is proportional to protein production. The YP production cellline also had a higher gene ratio and produced more protein than itsparent cell line, also suggesting that increasing gene copy is directlyrelated to increases in protein production. The data is presented inTable 8.

TABLE 8 Antibody Production Cell Line Invader Gene Ratio (Bot/YP) BotParent Cell Line 1.12 4.8 mg/ml  Bot Production Cell Line 3.03 55 mg/mlYP Parent Cell Line 1.32  4 mg/ml YP Production Cell Line 2.04 25 mg/ml

EXAMPLE 20 Transfection with Lentivirus Vectors

This example describes methods for the production of lentivirus vectorsand their use to infect host cells at a high multiplicity of infection.Replication-defective viral particles are produced by the transientcotransfection of the plasmids described in U.S. Pat. No. 6,013,516 in293T human kidney cells. All plasmids are transformed and grown in E.coli HB101 bacteria following standard molecular biology procedures. Fortransfection of eukaryotic cells, plasmid DNA is purified twice byequilibrium centrifugation in CsCl-ethidium bromide gradients. A totalof 40 μg DNA is used for the transfection of a culture in a 10 cm dish,in the following proportions: 10 μg pCMVΔR8, 20 μg pHR′, and 10 μg envplasmids, either MLV/Ampho, MLV/Eco or VSV-G. 293T cells are grown inDMEM supplemented with 10% fetal calf serum and antibiotics in a 10% CO₂incubator. Cells are plated at a density of 1.3×10⁶/10 cm dish the daybefore transfection. Culture medium is changed 4 to 6 hrs beforetransfection. Calcium phosphate-DNA complexes are prepared according tothe method of Chen and Okayama (Mol. Cell. Biol., 7:2745, 1987), andincubated overnight with the cells in an atmosphere of 5% CO₂. Thefollowing morning, the medium is replaced, and the cultures returned to10% CO₂. Conditioned medium is harvested 48 to 60 hrs aftertransfection, cleared of cellular debris by low speed centrifugation(300×g 10 min), and filtered through 0.45 μm low protein bindingfilters.

To concentrate vector particles, pooled conditioned medium harvested asdescribed above is layered on top of a cushion of 20% sucrose solutionin PBS and centrifuged in a Beckman SW28 rotor at 50,000×g for 90 min.The pellet is resuspended by incubation and gentle pipetting in 1-4 mlPBS for 30-60 min, then centrifuged again at 50,000×g for 90 min in aBeckmann SW55 rotor. The pellet is resuspended in a minimal volume(20-50 μl) of PBS and either used directly for infection or stored infrozen aliquots at −80° C.

The concentrated lentivirus vectors are titered and used to transfect anappropriate cell line (e.g., 293 cells, Hela cells, rat 208Ffibroblasts)) at a multiplicity of infection of 1,000. Analysis ofclonally selected cell lines expressing the exogenous protein willreveal that a portion of the selected cell lines contain more than twointegrated copies of the vector. These cell lines will produce more ofthe exogenous protein than cell lines containing only one copy of theintegrated vector.

EXAMPLE 21 Expression and Assay of G-protein Coupled Receptors

This example describes the expression of a G-Protein Coupled Receptorprotein (GPCR) from a retroviral vector. This example also describes theexpression of a signal protein from an IRES as a marker for expressionof a difficult to assay protein or a protein that has no assay such as aGPCR. The gene construct (SEQ ID NO: 34; FIG. 19) comprises aG-protein-coupled receptor followed by the IRES-signal peptide-antibodylight chain cloned into the MCS of pLBCX retroviral backbone. Briefly, aPvuII/PvuII fragment (3057 bp) containing the GPCR-IRES-antibody lightchain was cloned into the StuI site of pLBCX. pLBCX contains the EM7(T7) promoter, Blasticidin gene and SV40 polyA in place of the Neomycinresistance gene from pLNCX.

The gene construct was used to produce a replication defectiveretroviral packaging cell line and this cell line was used to producereplication defective retroviral vector. The vector produced from thiscell line was then used to infect 293GP cells (human embryonic kidneycells). After infection, the cells were placed under Blasticidinselection and single cell Blasticidin resistant clones were isolated.The clones were screened for expression of antibody light chain. The top12 light chain expressing clones were selected. These 12 light chainexpressing clones were then screened for expression of the GPCR using aligand binding assay. All twelve of the samples also expressed thereceptor protein. The clonal cell lines and there expression are shownin Table 9.

TABLE 9 Antibody Light Cell Clone Number Chain Expression GPCRExpression 4 + + 8 + + 13 + + 19 + + 20 + + 22 + + 24 + + 27 + + 30 + +45 + + 46 + + 50 + +

EXAMPLE 22 Multiple Infection of 293 Cells with Replication DefectiveRetroviral Vector

This example describes the multiple serial transfection of cells withretroviral vectors. The following gene construct was used to produce areplication defective retroviral packaging cell line.

5′ LTR=Moloney murine sarcoma virus 5′ long terminal repeat.EPR=Moloney murine leukemia virus extended packaging region.Blast=Blasticidin resistance gene.CMV=Human cytomegalovirus immediate early promoter.Gene=Gene encoding test proteinWPRE=RNA transport element3′ LTR=Moloney murine leukemia virus 3′ LTR.

This packaging cell line was then used to produce a replicationdefective retroviral vector arranged as follows. The vector was producedfrom cells grown in T150 flasks and frozen. The frozen vector was thawedat each infection. For infection # 3 a concentrated solution of vectorwas used to perform the infection. All other infections were performedusing non-concentrated vector. The infections were performed over aperiod of approximately five months by placing 5 ml of vector/mediasolution on a T25 flask containing 30% confluent 293 cells. Eight mg/mlof polybrene was also placed in the vector solution during infection.The vector solution was left on the cells for 24 hours and then removed.Media (DMEM with 10% fetal calf serum) was then added to the cells.Cells were grown to full confluency and passaged into a new T25 flask.The cells were then grown to 30% confluency and the infection procedurewas repeated. This process was repeated 12 times and is outlined Table10 below. After infections 1, 3, 6, 9 and 12, cells left over afterpassaging were used to obtain a DNA sample. The DNA was analyzed usingthe INVADER assay to determine an estimate of the number of vectorinserts in the cells after various times in the infection procedure. Theresults indicate that the number of vector insertions goes up over timewith the highest level being after the 12^(th) infection. Since a valueof 0.5 is approximately an average of one vector insert copy per cell,after twelve infections the average vector insert copy has yet to reachtwo. These data indicates that the average vector copy per cell is alittle less that 1.5 copies per cell. Also, there was no real change ingene copy number from infection #6 to infection #9. Furthermore, thesedata indicate that transfection conducted at a standard low multiplicityof infection fail to introduce more than one copy of the retroviralvector into the cells.

TABLE 10 Cell Line or Vector Titer “Invader” Gene Infection Number(CFU/ml) Ratio 293 0.053 Infection #1 1.05 × 10³ 0.39 Infection #2 1.05× 10³ Infection #3  7.6 × 10⁴ 0.45 Infection #4 1.05 × 10³ Infection #51.05 × 10³ Infection #6 1.05 × 10³ 0.54 Infection #7 1.05 × 10³Infection #8 1.05 × 10³ Infection #9 1.05 × 10³ 0.52 Infection #10 1.05× 10³ Infection #11 1.05 × 10³ Infection #12 1.05 × 10³ 0.69

EXAMPLE 23 Production of YP Antibody

This Example demonstrates the production of Yersinia pestis antibody bybovine mammary epithelial cells and human kidney fibroblast cells (293cells). Cells lines were infected with the α-LA YP vector. Both of thecell lines produced YP antibody. All of the antibody is active and theheavy and light chains are produced in a ratio approximating 1:1.

EXAMPLE 24 Transduction of Plant Protoplasts

This Example describes a method for transducing plant protoplasts.Tobacco protoplasts of Nicotiana tabacum c.v. Petit Havanna are producedaccording to conventional processes from a tobacco suspension culture(Potrykus and Shillito, Methods in Enzymology, vol. 118, Plant MolecularBiology, eds. A. and H. Weissbach, Academic Press, Orlando, 1986).Completely unfolded leaves are removed under sterile conditions from6-week-old shoot cultures and thoroughly wetted with an enzyme solutionof the following composition: Enzyme solution: H₂O, 70 ml; sucrose, 13g; macerozyme R 10, 1 g; cellulase, 2 g; “Onozuka” R 10 (Yakult Co.Ltd., Japan) Drisellase (Chemische Fabrik Schweizerhalle, Switzerland),0.13 g; and 2(n-morpholine)-ethanesulphonic acid (MES), 0.5 ml pH 6.0

Leaves are then cut into squares from 1 to 2 cm in size and the squaresare floated on the above-mentioned enzyme solution. They are incubatedovernight at a temperature of 26° C. in the dark. This mixture is thengently shaken and incubated for a further 30 minutes until digestion iscomplete.

The suspension is then filtered through a steel sieve having a meshwidth of 100 μm, rinsed thoroughly with 0.6M sucrose (MES, pH 5.6) andsubsequently centrifuged for 10 minutes at from 4000 to 5000 rpm. Theprotoplasts collect on the surface of the medium which is then removedfrom under the protoplasts, for example using a sterilized injectionsyringe.

The protoplasts are resuspended in a K₃ medium [sucrose (102.96 g/l;xylose (0.25 g/l); 2,4-dichlorophenoxyacetic acid (0.10 mg/l);1-naphthylacetic acid (1.00 mg/l); 6-benzylaminopurine (0.20 mg/i); pH5.8](Potrykus and Shillito, supra) that contains 0.4M sucrose.

To carry out the transformation experiments, the protoplasts are firstof all washed, counted and then resuspended, at a cell density of from 1to 2.5×10⁶ cells per ml, in a W₅ medium [154 mM NaCl, 125 mM CaCl₂×2H₂O,5 mM KCl, 5 mM glucose, pH 5.6), which ensures a high survival rate ofthe isolated protoplasts. After incubation for 30 minutes at from 6 to8° C., the protoplasts are then used for the transduction experiments.

The protoplasts are exposed to a pseudotyped retroviral vector (e.g., alentiviral vector) encoding a protein of interest driven by a plantspecific promoter. The vector is prepared as described above and is usedat an MOI of 1,000. The protoplasts are then resuspended in fresh K₃medium (0.3 ml protoplast solution in 10 ml of fresh K₃ medium). Furtherincubation is carried out in 10 ml portions in 10 cm diameter petridishes at 24° C. in the dark, the population density being from 4 to8×10₄ protoplasts per ml. After 3 days, the culture medium is dilutedwith 0.3 parts by volume of K₃ medium per dish and incubation iscontinued for a further 4 days at 24° C. and 3000 lux of artificiallight. After a total of 7 days, the clones that have developed from theprotoplasts are embedded in nutrient medium that contains 50 mg/l ofkanamycin and has been solidified with 1% agarose, and are cultured at24° C. in the dark in accordance with the “bead-type” culturing method(Shillito, et al., Plant Cell Reports, 2, 244-247 (1983)). The nutrientmedium is replaced every 5 days by a fresh amount of the same nutrientsolution. Analysis of the clones indicates that express the gene ofinterest.

EXAMPLE 25 Stability of Vector Insertions in Cell Lines Over Time

Two cell lines that contain gene inserts of the LN-CMV-Bot vector wereanalyzed for there ability to maintain the vector inserts over a numberof passages with and without neomycin selection. The first cell line isa bovine mammary epithelial cell line that contains a low number ofinsert copies. The second cell line is a 293GP line that containsmultiple copies of the vector insert. At the start of the experiment,cell cultures were split. This was at passage 10 for the bovine mammaryepithelial cells and passage 8 for the 293GP cells. One sample wascontinually passaged in media containing the neomycin analog G418, theother culture was continually passaged in media without any antibiotic.Every 3-6 passages, cells were collected and DNA was isolated fordetermination of gene ratio using the INVADER assay. Cell werecontinually grown and passaged in T25 flasks. The results of the assaysare shown below:

TABLE 11 Low Gene Copy Cell Line INVADER Gene Cell Line and TreatmentPassage Number Ratio BMEC/Bot #66 + G418 10 0.67 BMEC/Bot #66 − G418 100.89 BMEC/Bot #66 + G418 16 0.67 BMEC/Bot #66 − G418 16 0.64 BMEC/Bot#66 + G418 21 0.62 BMEC/Bot #66 − G418 21 0.58 BMEC/Bot #66 + G418 270.98 BMEC/Bot #66 − G418 27 0.56 BMEC/Bot #66 + G418 33 0.80 BMEC/Bot#66 − G418 33 0.53

TABLE 12 High Gene Copy Cell Line Cell Line and Treatment Passage NumberINVADER Gene Ratio 293GP/Bot #23 + G418 8 3.46 293GP/Bot #23 − G418 83.73 293GP/Bot #23 + G418 14 3.28 293GP/Bot #23 − G418 14 3.13 293GP/Bot#23 + G418 17 3.12 293GP/Bot #23 − G418 17 2.91 293GP/Bot #23 + G418 223.6 293GP/Bot #23 − G418 22 2.58 293GP/Bot #23 + G418 28 2.78 293GP/Bot#23 − G418 28 3.44 293GP/Bot #23 + G418 36 2.6 293GP/Bot #23 − G418 362.98

These data show that there are no consistent differences in gene ratiobetween cells treated with G418 and those not treated with antibiotic.This suggests that G418 selection is not necessary to maintain thestability of the vector gene insertions. Also, these vector insertsappear to be very stable over time.

All publications and patents mentioned in the above specification areherein incorporated by reference. Various modifications and variationsof the described method and system of the invention will be apparent tothose skilled in the art without departing from the scope and spirit ofthe invention. Although the invention has been described in connectionwith specific preferred embodiments, it should be understood that theinvention as claimed should not be unduly limited to such specificembodiments. Indeed, various modifications of the described modes forcarrying out the invention which are obvious to those skilled inmolecular biology, protein fermentation, biochemistry, or related fieldsare intended to be within the scope of the following claims.

SEQUENCE LISTING <110> Bleck, Gregory

-   -   Bremel, Robert    -   Miller, Linda    -   York, Donna

<120> Host Cells Containing Multiple Integrating Vectors <130>GALA-04198

<150> 60/215,925<151> 2000-07-03<160> 36<170> PatentIn version 3.0<210> 1<211> 2101

1. A host cell comprising a genome, said genome comprising at least twointegrated integrating vectors, wherein said integrating vectorscomprise at least one exogenous gene operably linked to a promoter. 2.The host cell of claim 1, wherein said integrating vectors furthercomprise a secretion signal sequence operably linked to said exogenousgene.
 3. The host cell of claim 1, wherein said integrating vectorsfurther comprise an RNA stabilizing element operably linked to saidexogenous gene.
 4. The host cell of claim 1, wherein said integratingvectors comprise at least two exogenous genes.
 5. The host cell of claim4, wherein said at least two exogenous genes are arranged in apolycistronic sequence.
 6. The host cell of claim 5, wherein said atleast two exogenous genes are separated by at least one internalribosome entry site.
 7. The host cell of claim 5, wherein two exogenousgenes are arranged in said polycistronic sequence.
 8. The host cell ofclaim 7, wherein said two exogenous genes encode a heavy chain of animmunoglobulin molecule and a light chain of an immunoglobulin molecule.9. The host cell of claim 4, wherein one of said at least two exogenousgenes is a selectable marker.
 10. The host cell of claim 1, wherein saidintegrating vector is a retroviral vector.
 11. The host cell of claim10, wherein said retrovirus vector is a pseudotyped retroviral vector.12. The host cell of claim 11, wherein said pseudotyped retroviralvector comprises a G glycoprotein.
 13. The host cell of claim 12,wherein the G glycoprotein is selected from the group consisting ofvesicular stomatitis virus, Piry virus, Chandipura virus, Spring viremiaof carp virus and Mokola virus G glycoproteins.
 14. The host cell ofclaim 10, wherein said retroviral vector comprises long terminal repeatsselected from the group consisting of MoMLV, MoMuSV, and MMTV longterminal repeats.
 15. The host cell of claim 11, wherein said retroviralvector is a lentiviral vector.
 16. The host cell of claim 15, whereinsaid lentiviral vector comprises long terminal repeats selected from thegroup consisting of HIV and equine infectious anemia virus long terminalrepeats.
 17. The host cell of claim 1, wherein said host cell is presentin a culture system selected from the group consisting of in vitro andin vivo cultures.
 18. The host cell of claim 1, wherein said host cellis selected from Chinese hamster ovary cells, baby hamster kidney cells,and bovine mammary epithelial cells.
 19. The host cell of claim 1,wherein said host cell is clonally derived.
 20. The host cell of claim1, wherein said host cell is non-clonally derived.
 21. The host cell ofclaim 1, wherein genome is stable for greater than 10 passages.
 22. Thehost cell of claim 21, wherein said genome is stable for greater than 50passages.
 23. The host cell of claim 21, wherein said genome is stablefor greater than 100 passages.
 24. The host cell of claim 1, whereinsaid integrated exogenous gene is stable in the absence of selection.25. The host cell of claim 1, wherein said promoter is selected from thegroup consisting of alpha-lactalbumin promoter, cytomegalovirus promoterand the long terminal repeat of Moloney murine leukemia virus.
 26. Thehost cell of claim 1, wherein said at least one exogenous gene isselected from the group consisting of genes encoding antigen bindingproteins, pharmaceutical proteins, kinases, phosphatases, nucleic acidbinding proteins, membrane receptor proteins, signal transductionproteins, ion channel proteins, and oncoproteins.
 27. The host cell ofclaim 1, wherein said genome comprises at least 3 integrated integratingvectors.
 28. The host cell of claim 1, wherein said genome comprises atleast 4 integrated integrating vectors.
 29. The host cell of claim 1,wherein said genome comprises at least 5 integrated integrating vectors.30. The host cell of claim 1, wherein said genome comprises at least 7integrated integrating vectors.
 31. The host cell of claim 1, whereinsaid genome comprises at least 10 integrated integrating vectors. 32.The host cell of claim 1, wherein said genome comprises at least 20integrated integrating vectors.
 33. The host cell of claim 1, whereinsaid genome comprises at least 1000 integrated integrating vectors. 34.The host cells of claim 1, further comprising at least 2 integratedcopies of a first integrating vector comprising a first exogenous gene,and at least 1 integrated copy of a second integrating vector comprisinga second exogenous gene.
 35. The host cell of claim 1, wherein said hostcell expresses greater than about 10 picograms of said exogenous proteinper day.
 36. A method for transfecting host cells comprising: 1)providing: a) a host cell comprising a genome, and b) a plurality ofintegrating vectors; and 2) contacting said host cell with saidplurality of integrating vectors under conditions such that at least twointegrating vectors integrate into said genome of said host cell. 37.The method of claim 36, wherein said conditions comprise contacting saidhost at a multiplicity of infection of greater than
 10. 38. The methodof claim 36, wherein said conditions comprise contacting said host at amultiplicity of infection of from about 10 to
 1000. 39. The method ofclaim 36, wherein said host cells are contacted with said plurality ofintegrating vectors under conditions such that at least 3 integratingvectors integrate into said genome of said host cell.
 40. The method ofclaim 36, wherein said host cells are contacted with said plurality ofintegrating vectors under conditions such that at least 4 integratingvectors integrate into said genome of said host cell.
 41. The method ofclaim 36, wherein said host cells are contacted with said plurality ofintegrating vectors under conditions such that at least 5 integratingvectors integrate into said genome of said host cell.
 42. The method ofclaim 36, wherein said host cells are contacted with said plurality ofintegrating vectors under conditions such that at least 7 integratingvectors integrate into said genome of said host cell.
 43. The method ofclaim 36, wherein said host cells are contacted with said plurality ofintegrating vectors under conditions such that at least 10 integratingvectors integrate into said genome of said host cell.
 44. The method ofclaim 36, wherein said integrating vectors comprise at least oneexogenous gene operably linked to a promoter
 45. The method of claim 36,wherein said integrating vectors further comprise a secretion signalsequence operably linked to said exogenous gene.
 46. The method of claim36, wherein said integrating vectors further comprise an RNA stabilizingelement operably linked to said gene exogenous gene.
 47. The method ofclaim 36, wherein said integrating vectors comprises at least twoexogenous genes.
 48. The method of claim 47, wherein said at least twoexogenous genes are arranged in a polycistronic sequence.
 49. The methodof claim 36, wherein said integrating vector is a retroviral vector. 50.The method of claim 49, wherein said retroviral vector is a pseudotypedretroviral vector.
 51. The method of claim 49, wherein said retroviralvector is a lentiviral vector.
 52. The method of claim 51, wherein saidlentiviral vector is a pseudotyped lentivirus vector comprising a Gglycoprotein.
 53. The method of claim 36, wherein said host cell isselected from Chinese hamster ovary cells, baby hamster kidney cells,and bovine mammary epithelial cells.
 54. The method of claim 36, furthercomprising clonally selecting said transfected host cells.
 55. Themethod of claim 36, further comprising transfecting said host cells withat least two integrating vectors, each of said two integrating vectorscomprising a different exogenous gene.
 56. A method of producing aprotein of interest comprising: 1) providing a host cell comprising agenome, said genome comprising at least two integrated copies of atleast one integrating vector comprising an exogenous gene operablylinked to a promoter, wherein said exogenous gene encodes a protein ofinterest, and 2) culturing said host cells under conditions such thatsaid protein of interest is produced.
 57. The method of claim 56,wherein said integrating vector further comprises a secretion signalsequence operably linked to said exogenous gene.
 58. The method of claim56, further comprising step 3) isolating said protein of interest. 59.The method of claim 57, wherein said conditions are selected from thegroup consisting of roller bottle cultures, perfusion cultures, batchfed cultures, and petri dish cultures.
 60. The method of claim 56,wherein said genome of said host cell comprises greater than 3integrated copies of said integrating vector.
 61. The method of claim56, wherein said genome of said host cell comprises greater than 4integrated copies of said integrating vector.
 62. The method of claim56, wherein said genome of said host cell comprises greater than 5integrated copies of said integrating vector.
 63. The method of claim56, wherein said genome of said host cell comprises greater than 7integrated copies of said integrating vector.
 64. The method of claim56, wherein said genome of said host cell comprises greater than 10integrated copies of said integrating vector.
 65. The method of claim56, wherein said genome of said host cell comprises between about 2 and20 integrated copies of said integrating vector.
 66. The method of claim56, wherein said genome of said host cell comprises between about 3 and10 integrated copies of said integrating vector.
 67. The method of claim56, wherein said integrating vector is a retroviral vector.
 68. Themethod of claim 67, wherein said retroviral vector is a pseudotypedretroviral vector.
 69. The method of claim 67, wherein said retroviralvector is a lentiviral vector.
 70. The method of claim 56, wherein saidhost cell is selected from Chinese hamster ovary cells, baby hamsterkidney cells, and bovine mammary epithelial cells.
 71. The method ofclaim 56, wherein said host cells synthesize greater than about 1picograms per cell per day of said protein of interest.
 72. The methodof claim 56, wherein said host cells synthesize greater than about 10picograms per cell per day of said protein of interest.
 73. The methodof claim 56, wherein said host cells synthesize greater than about 50picograms per cell per day of said protein of interest.
 74. The methodof claim 56, wherein said cells are clonally selected.
 75. A method forscreening compounds comprising: 1) providing: a) providing a host cellcomprising a genome, said genome comprising at least two integratedcopies of at least one integrating vector comprising an exogenous geneoperably linked to a promotor, wherein said exogenous gene encodes aprotein of interest; and b) one or more test compounds; 2) culturingsaid host cells under conditions such that said protein of interest isexpressed; 3) treating said host cells with said one or more testcompounds; and 4) assaying for the presence of a response in said hostcells to said test compound.
 76. The method of claim 75 wherein saidexogenous gene encodes a protein selected from the group consisting ofmembrane receptor proteins, nucleic acid binding proteins, cytoplasmicreceptor proteins, ion channel proteins, signal transduction proteins,protein kinases, protein phosphatases, and proteins encoded byoncogenes.
 77. The method of claim 76, wherein said host cell furthercomprises a reporter gene.
 78. The method of claim 77, wherein saidreporter gene is selected from the group consisting of green fluorescentprotein, luciferase, beta-galactosidase, and beta-lactamase.
 79. Themethod of claim 75, wherein said assaying step further comprisingdetecting a signal from said reporter gene.
 80. The method of claim 75,wherein said genome of said host comprises at least two integratingvectors, wherein each of said at least two integrating vectors comprisesa different exogenous gene.
 81. The method of claim 75, wherein saidintegrating vector is a pseudotyped retroviral vector.
 82. The method ofclaim 75, wherein said host cell is selected from chinese hamster ovarycells, baby hamster kidney cells, and bovine mammary epithelial cells.83. A method for comparing protein function comprising: 1) providing a)a first host cell comprising a first integrating vector comprising apromoter operably linked to a first exogenous gene, wherein said firstexogenous gene encodes a first protein of interest; b) at least a secondhost cell comprising a second integrating vector comprising a promoteroperably linked to a second exogenous gene, wherein said secondexogenous gene encodes a second protein of interest that is a variant ofsaid first protein of interest; 2) culturing said host cells underconditions such that said first and second proteins of interest areproduced; and 3) comparing the activities of said first and secondproteins of interest.
 84. The method of claim 83, wherein said exogenousgene encodes a protein selected from the group consisting of membranereceptor proteins, nucleic acid binding proteins, cytoplasmic receptorproteins, ion channel proteins, signal transduction proteins, proteinkinases, protein phosphatases, cell cycle proteins, and proteins encodedby oncogenes.
 85. The method of claim 83, wherein said first and secondproteins of interest differ by a single nucleotide polymorphism.
 86. Themethod of claim 83, wherein said first and second proteins of interestare greater than 95% identical.
 87. The method of claim 83, wherein saidfirst and second proteins of interest are greater than 90% identical.88. The method of claim 83, wherein said genomes of said first andsecond host cells each comprise greater than 3 integrated copies of saidintegrating vector.
 89. The method of claim 83, wherein said genomes ofsaid first and second host cells each comprise greater than 4 integratedcopies of said integrating vector.
 90. The method of claim 83, whereinsaid genomes of said first and second host cells comprises greater than5 integrated copies of said integrating vector.
 91. The method of claim83, wherein said integrating vector is a retroviral vector.
 92. Themethod of claim 91, wherein said retrovirus vector is a pseudotypedretroviral vector.
 93. The method of claim 91, wherein said retroviralvector is a lentiviral vector.
 94. A method comprising: 1) providing: a)a host cell comprising a genome comprising at least one integratedexogenous gene; and b) a plurality of integrating vectors; and 2)contacting said host cell with said plurality of integrating vectorsunder conditions such that at least two of said integrating vectorsintegrate into said genome of said host cell.
 95. The method of claim94, wherein said integrated exogenous gene comprises an integratingvector.
 96. The method of claim 94, wherein said host cell is clonallyselected.
 97. The method of claim 94, wherein said host cell isnon-clonally selected.
 98. The method of claim 94, wherein saidconditions comprise contacting said host at a multiplicity of infectionof greater than
 10. 99. The method of claim 94, wherein said conditionscomprise contacting said host at a multiplicity of infection of fromabout 10 to
 1000. 100. The method of claim 94, wherein said host cellsare contacted with said plurality of integrating vectors underconditions such that at least 3 integrating vectors integrate into saidgenome of said host cell.
 101. The method of claim 94, wherein saidintegrating vector is a retroviral vector.
 102. The method of claim 101,wherein said retroviral vector is a pseudotyped retroviral vector.